Keeping The Faith
by Pilgrim Soul
Summary: Sheppard goes missing and his friends try to move on without him but soon Atlantis is facing a new threat. Shep whump. ShepMcKayWeir friendship. Rated for violence.
1. Prologue

_**Disclaimer: **I do not own Stargate Atlantis or any of it's characters, I'm just playing with them for a while. _

_**Beta:** The wonderful Alipeeps who's help has been invaluable._

_**Characters:** Sheppard, McKay and Weir. Friendship not 'ship._

_**Spoilers:** Lets just say up to the end of season two to be on the safe side._

_**Warnings:** The T rating is for violence, if you are particularly squeamish this may not be the fic for you, please bear that in mind.  
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**Keeping the Faith**

**Prologue**

Sheppard watched with a smile. He was used to seeing McKay over-excited at the discovery of hitherto unknown Ancient ruins, but it amused him to see the normally calm Doctor Elizabeth Weir so animated; she was clearly relishing the time away from her desk and he hadn't seen her laugh so much in weeks. It was not often she got a chance to come off-world, so when the Guennec people had discovered these ruins following a landslide, and invited the Atlanteans to help their own historians study them, it was an ideal opportunity for her.

She would be heading back to Earth with the Daedalus in a few days and for the last fortnight had immersed herself in writing reports for the review board; he'd had to write several himself and he knew just how mind-numbing it was. Deciding along with Rodney that she had spent way too much time in her office lately, they'd made it their mission to talk her into coming along; though he suspected she only feigned reluctance in the first place to maintain an air of professionalism. So here they all were, enjoying the sunshine and the amiable company of the Guennec while Colonel Caldwell was playing big boss of Atlantis for the day.

Sitting down off to one side of the site, he took a drink from his canteen. The sun was warm, the sky was blue and no one was trying to kill him; it was turning out to be a good day. He looked around at the rest of his team. He'd expected Ronon to be bored out of his mind, and initially he had been, but he'd perked up with the arrival of an attractive young Guennec archaeologist and had been lifting and carrying for her ever since. Sheppard had to admit it was actually quite sweet to watch the big man acting like a teenager with a crush.

McKay was his usual bundle of nervous energy, but his enthusiasm had been dampened by the apparent lack of any kind of energy reading coming from the ruins. His grumbling had become increasingly irritating. As brilliant as he was, Rodney had, at times, all the emotional maturity of an eight year old.

Teyla was on babysitting duties with the scientist and John watched her fondly as she helped McKay; she had the patience of a saint and needed it. He knew that, if he, Ronan and McKay were left to their own devices for too long, they'd probably kill each other; Teyla was the one who both counselled them and knocked their heads together when it was needed. Moreover, he had to admit, she could probably kick all their asses if she had the mind to.

He surveyed the scene in front of him happily. If someone had told him just a few years ago that this bunch of oddballs would be his dearest friends, his family, he wouldn't have believed them; but back then he had been a different John Sheppard. Smiling contentedly, he lay back, resting his head against a fallen tree, and looked up at the perfect blue sky.

"You idiot!" McKay's voice broke through the gentle background murmur of the day. Sheppard sighed and sat up. Ronon was staring daggers at the scientist, who was ranting while gesticulating gesturing angrily at something on the ground. Getting resignedly to his feet, he made his way over to join them.

"Rodney, I am sure Ronon did not mean to. Did you Ronon?" Teyla, forever the peacemaker.

"He shouldn't have left it in such a stupid place," answered the Satedan.

"Well you'd know all about stupidity, wouldn't you?" countered the scientist. Ronon took a step forward; Teyla put her hand on his chest and gave him her best warning look.

Sheppard jogged up and he looked at the ground where the source of the argument lay. It was a rock; he looked up enquiringly. Ronon put his foot on the rock and rolled it over to reveal what was left of Rodney's laptop.

"Ah!"

"Ah? Is that all you can say? This…" Rodney waved his hands wildly while searching for an appropriate word, "…Neanderthal has just lost me an entire morning's work."

"I was trying to help clear the rocks out of the way."

"No, you were trying to impress your little friend over there." McKay pointed at the embarrassed young archaeologist while attempting to mimic Ronon's voice. "Me strong. Me carry rocks!"

Sheppard sighed and looked at Teyla with a pleading expression. Getting the message she took a firm hold of Ronon's arm and led him away before he got the urge to drop a rock on the scientist's head, meanwhile the Colonel put his arm around McKay's shoulder and led him away in the opposite direction toward Elizabeth.

"Problems?"

"Rodney and Ronon just had a little disagreement. But everything's fine now." McKay was sulking. "Isn't it Rodney?" His voice made it clear that things would be fine whether the Canadian liked it or not and he got a mumbled reply. _Yeah! Definitely an eight year old_. Sheppard rolled his eyes at Elizabeth; he could see she was trying not to laugh.

"I was about to come and ask for your advice on something actually, Rodney."

"Really?" He asked quietly, tilting his head slightly and feigning disinterest.

"Yes, it's got the rest of us completely stumped."

"Oh! Well," he said, perking up a bit. "I'm sure I'll be able to help."

"Well then, you two go and do what ever it is you're doing and I'll take a quick jog back to the jumper and get you the spare laptop." Mouthing a thank you to Elizabeth, John/Sheppard set off on the short trip back to the jumper.

It was too nice a day to hurry so he walked leisurely back up the gorge, making the most of the peace and quiet; it had been a while since he'd been able to relax like this and Guen was a beautiful planet. He'd only gone only about five hundred yards from the site, just into the trees at the top of the gorge, when he heard the noise behind him. Stopping dead he listened, instinct taking over; again he heard movement. It was probably just a wild animal of some kind, he thought, but that didn't mean he wasn't going to be cautious. Shifting his grip on his P-90, he began to move warily around to where he thought he'd heard the noise, making sure he kept close to cover in case he needed it. Suddenly there was a burst of movement from the bushes just a few feet in front of him. On instinct he raised the P-90 and found himself staring his attacker in the face. A child of about eleven looked back at him. Letting out the breath he'd been holding with a relieved chuckle, he lowered the gun.

"You scared the hell out of me." He smiled at the child who just stared back unmoving. "I guess I probably scared you too huh?" He took a step forward, bending down slightly to make eye contact. "Hey! You okay?" He barely had time to register the weapon in the child's hand before the pain hit him. He fell face first to the ground, gasping for breath, his throat constricted, his whole body screaming in pain.

_What the hell just happened? _His chest was tight and his muscles convulsing, he managed to raise his head and his young assailant still stood there studying him without emotion. The boy's head suddenly snapped up, his attention now on something behind his victim; gathering all of his strength Sheppard started to push himself up only to feel a boot in between his shoulder blades; and he was slammed back to the ground.

The weapon was fired at him a second time and the pain was like fire inside him, and the world slowed down, silence enveloped him and slowly blackness took over.


	2. Train Keeps A Rollin’

_A/N: Thank you so much for your positive comments. Now I'm a little bit worried that you will find the first couple of chapters to be slightly disjointed but if you bear with me things start to flow better. There's a fine line between giving enough detail and boring the reader rigid hopefully for the most part I've stayed on the right side of that line.  
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**Chapter 1**

**Train Keeps A Rollin'**

He couldn't see the face of the man talking; a bag was thrown over his head and his arms were bound behind him. Laying on his side against the cold stone, he felt light headed; the cloth of the bag was humid with his breath and sweat. The rasping voice of the priest had stopped and been replaced by the soft tones of another man, this man didn't shout or rant, his voice was almost soothing, genial; but what he said wasn't.

"You wish to know what became of your friends? Yes? Very well. We killed them." Sheppard felt his chest tightening; it made sense, that was why they hadn't come for him.

"Once they noticed you missing, the two warriors, Dex and the Athosian woman, split up to find you. From our vantage point higher up the gorge it was easy for our men to pick them off, their concern for you made them careless." He tried to force the emotion down, replace it with anger but found that the only anger he felt was directed at himself. He curled himself into a ball, wishing he could block the words out, but needing to hear them at the same time. "Once they were taken care of, we attacked the others. The Guennec are not military minded, they barely put up a fight. But McKay and Weir, they died valiantly, I will say that for your doctors, each begging for the other's life. You should be proud of them. In the end we killed the man first, it seemed only right that as your leader Doctor Weir should be the last to die. She never faltered, she remained defiant right up until we put the bullet in her head; an extraordinary woman." The voice paused, letting the words settle before continuing.

"Since then we have made several successful attacks. I won't lie to you we have suffered losses also, but none as devastating as those your people face. So you see by refusing to tell us what we want to know, you are just delaying the inevitable. And in doing so you will sentence more of your people to their deaths."

But Sheppard couldn't answer, in fact he barely heard the last words the man said; his mind was filled with the images of his friends dying, their blood spilled. Ronon's and Teyla's broken bodies, Elizabeth and Rodney trying to save one another, that's exactly what they would do, McKay braver than he knew, Elizabeth strong to the last. They were his responsibility, his greatest fear in life was that he would fail them, but that was exactly what had happened. His friends were gone and he hadn't been there for them, he'd been careless and stupid in letting these people take him so easily and the people he cared for most had paid the price.

ooOoo

It had been almost an hour before anyone had missed him. Remembering that fact was painful for Elizabeth; how could they have been so stupid? They had all been busy with their work, she hadn't even realised that so much time had passed. Rodney had forgotten all about his laptop and had commandeered hers. Ronon had returned to his flirting with the young archaeologist. It was Teyla who first voiced her concern and as soon as she had pointed out the Colonel's absence Elizabeth knew something was wrong and she knew by the tension in the rest of his team that they also sensed it. Ronon and Teyla took off almost immediately; they found the puddle jumper where they had left it, still cloaked and untouched. None of the inhabitants of the nearby settlement had seen him; no one had reported any Wraith activity and Teyla had not sensed their presence.

The Guennec chancellor Lewyn had offered up every assistance he could, many of the Guennec people had joined the search efforts themselves; Caldwell had taken the Daedalus and scanned the planet from orbit, but Colonel Sheppard was no longer there. McKay had come up with a possible gate destination but that had just led them on a wild goose chase. They had asked all friendly races to pass on any information they might hear and Teyla and Ronon had worked tirelessly, travelling to trading planets and talking to the ordinary citizens instead of governments and councils, hoping beyond hope that someone, somewhere knew what had become of their commander but, despite their best efforts, they had discovered nothing. It was as if John Sheppard had disappeared into thin air.

In the forest, Ronon had found the area where he believed Sheppard had been ambushed; there were drag marks in the soft forest floor heading back toward the gate. She told herself that the fact they had taken him with them was a sign that he was still alive, even though her rational mind told her that wasn't necessarily the case, and her previous life working for the UN had given her far too great an understanding of the horrors that awaited some hostages.

The return to Earth had been delayed so the Daedalus could help with the search, but in a few hours Elizabeth and Colonel Caldwell would begin the slow journey back to Earth. She would meet with the international committee and debrief them on the progress of the Atlantis expedition exactly as had been planned. Sheppard was to have stayed behind, so at least one of them would have been there should any crisis arise, but he had become the crisis, and now Rodney would take command of Atlantis in his stead.

Everyone knew that Rodney blamed himself but few realised how much guilt she carried. It was difficult knowing that, while she had been standing in the sunshine, running her hands across the cool, pale stone of the ruins, laughing and joking with her companions and feeling more relaxed, more free than she had in months, somewhere in the trees above the gorge John had been taken from them.

She wondered how it had happened. He hadn't fired his gun, so they must have taken him by surprise. Did he know what was happening to him? Had he tried to call out for them? Was he in pain? Was he dead? She'd heard people say about the missing that not knowing was the worst thing, now she knew that it was true. Of course, Sheppard and his team had gone missing before, as had Lorne's team, but never for so long, never leaving her feeling so powerless.

Elizabeth watched from the control room balcony as Ronon and Teyla returned through the gate; she didn't have to ask if their mission had been successful, she could tell by the tired expressions on their faces that they had drawn another blank. With each passing day that the teams returned with no news, the city felt a little emptier.

The Satedan glanced up at her, making eye contact enough to convey his frustration and regret at not being able to bring better news, and turned and headed across the gate room, leaving Teyla standing alone. Elizabeth smiled at the Athosian who wearily walked up the stairs to join her.

"I am sorry, we had hoped that the traders we saw today would know something, they travel to many worlds."

"It's okay. I think if we're gong to find anything out now it will be down to luck rather than anything else." She gestured in the direction Ronon had gone. "He's taking this hard, isn't he?"

"Yes." Teyla nodded. "Without Sheppard, I doubt he would have stayed here so long. There is a certain affinity between them." Elizabeth smiled at the comment; on the surface there was little resemblance between the hulking, brooding form of the runner and the lean frame and boyish exuberance of the Colonel but Teyla was right, the two of them had identified with each other from the start.

"Will he stay?" She'd been concerned that Ronon wouldn't stay on Atlantis now; he and Caldwell had a fragile respect for one another but, assuming that the Colonel was given command of the city, she was unsure if they would see eye to eye on things. Ronon was unpredictable and that wasn't a trait the military liked to encourage. John had understood Ronon but Caldwell was a by the book kind of soldier; Elizabeth suspected John had gotten bored of the book by chapter two and had gone off to do something fun instead.

"I believe he will for the time being, he has no where else to go." She sighed. "But in time, I can not say, he is…stubborn."

"I'd noticed. Try and talk to him; let him know he's needed around here."

"I will try." To Elizabeth's surprise, Teyla leant forward and hugged her. "I may not see you again before you leave, so I shall say goodbye now. May you have a safe and swift journey." She pulled back and smiled. "You shall be missed."

"Thank you, Teyla." Elizabeth watched her the Athosian leave; she was slowly coming to realise that the two of them were not so very different. Teyla knew the pressures of being a leader, of trying to balance heart and mind to do what's best for your people; she also understood that sometimes you found yourself torn between the two.

"Elizabeth?" Carson stepped up beside her. "Are you okay love?" She exhaled heavily.

"I'm fine." He looked at her with his patented doctor expression, one full of concern, and disbelief at anything his patients told him, especially if they said they were 'fine'. "I feel like I'm abandoning ship."

"Nobody thinks that. And you'll be back in a few weeks."

"I want to be here. If we find him, I want to be here, even if it's just to mourn him. Atlantis is a family and…"

"And Colonel Sheppard is the annoying older brother?" Carson offered. She looked at him with an affectionate smile and breathed out a laugh.

"Something like that. Annoying in an endearing kind of way though."

"Aye, you couldn't help but like the man, even if you could cheerfully throttle him half the time." Elizabeth gripped the railing tight, her voice tired.

"We're already talking about him like he's dead." Frustration and exhaustion filled her eyes. "We've given up on him."

"No one's giving up on him, we never will, but at the same time we can't put our lives on hold. We all have responsibilities Elizabeth, and right now yours are back on Earth." He reached out, putting his hand over hers and giving it a gentle squeeze. "If we hear anything we'll send a data stream right away, I promise."

"I know you will. Thank you, Carson." And, with one last glance at the gate, she turned and walked away, leaving a worried Carson behind her.

ooOoo

The priest roared with frustration and another blow landed against his kidneys. Sheppard felt his body convulse slightly at the strike but withdrew further in to himself, blocking it out, pushing his mind somewhere else.

"_I hear the train a comin', it's rolling round the bend and I ain't seen the sunshine since I don't know when_…_" _Filling his mind with the words, he blanked out everything else. The next kick hit him in the side of the head, causing him to roll over; lights danced behind his eyelids and he sang out louder. "_I'm stuck in Folsom prison, and time keeps draggin' on, but that train keeps a rollin' on down to San Anton..."_

"Careful Patriarch, you will damage his mind and then he will never be of any use to us." The calm voice of the soldier was faint beneath the roaring of the blood in his ears.

"I'm beginning to think his mind is already damaged." The priest breathed heavily, huffing and wheezing like a wild animal.

"_When I was just a baby my mama told me. Son, always be a good boy, don't ever play with guns."_

"Then let us try a different approach. We are in no hurry."

"Your methods have only succeeded in making him less responsive. What is he doing?"

"_But I shot a man in Reno just to watch him die, now every time I hear that whistle I hang my head and cry…"_

"I believe he is singing, sir." There was a hint of amusement in his voice. The priest practically growled but John suspected it was aimed as much at the guard as it was him.

"_I bet there's rich…" _Another brutal kick landed against his ribs, briefly knocking the wind out of him._ "…folks eating in a fancy dining car." _He was becoming breathless but still kept going. Hands grabbed his throat and pinned him to the floor. He could smell the priest's sweat as he fought to breathe, gasping in small pockets of air. The pressure increased and he could feel his lungs burning for oxygen.

"Patriarch, you're killing him. He will be of no use to us dead." _Dead. _The unseen guard was right, he would be of no use to them dead so he stopped struggling and let himself drift away.


	3. Shooting The Messenger

_A/N_ - _Firstly I just want to rectify my mistake in omitting to tell you that the song Shep was singing in the last chapter was Folsom Prison Blues by (of course) Johnny Cash. Secondly, I'm afraid I can't comment on any reviews left because I haven't been unable to view them but please don't let that stop you from leaving them, all feedback is most welcome especially as this is my first fic.  
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_With this chapter I'm going to really annoy you all because it's (a) incredibly short (even by my standards) & (b) no Shep. Sorry again! This may seem a little bit out of place and I did think about removing this aspect of the story, but in the end decided to leave it in. To make it up to you I'll post the next chapter up later this evening. After that the rate of updates will slow down a bit I'm afraid but I'll try to not keep you hanging too long.  
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**Chapter 2**

**Shooting The Messenger **

She parked the hire car at the top of the road and walked, hoping to clear her head, or maybe just delay the moment. She didn't have to be here, could have left it to someone else, but she had insisted; she wanted to be the one to do this, needed to be the one. That did not, however, make it any easier. The wind whipped the fallen leaves up into little whirlpools around her feet. It was a beautiful day; the kind of perfect autumn day where the sky was high and pale and you could taste winter in the air.

Part of her wanted to keep walking, just go straight past and carry on, but where would she go? Earth was no longer her home. She looked around at the old lady pruning the roses on her porch and the kids playing an improvised version of baseball in the street and thought, if only they knew. If only they knew, the places I've been, the things I've seen, the things I've done. She was an alien visitor on the planet of her birth, her home far away beyond the stars. A sudden feeling of loneliness washed over her. Swallowing back hard and closing her eyes, she drew in a deep breath of the cold air, trying to calm the tightening knot in her stomach.

The house she was looking for was at the end of the avenue, every bit as picture perfect as its neighbours. She hesitated for a moment before walking up the path, then walked quickly to the door and rang the bell. She stood and waited; a minute passed before she saw a shadow moving through the frosted glass. She had rehearsed this moment a hundred times in her mind but now it was here she suddenly felt unsure. Part of the reason she held the position she did now was down to her communication skills but they deserted her when the door in front of her opened and she found herself looking into hazel eyes.

ooOoo

The house was as impeccably neat on the inside as it was on the outside but still had a lived in feel to it; most of the furniture had seen better days but was lovingly cleaned and polished all the same. In the lounge a large dresser against the wall displayed an array of photographs; a younger version of the Colonel standing in uniform beside a small woman with curly blonde hair carrying a simple posy of flowers. The life story of a young woman unfolded through a series of photographs from childhood to graduation to blushing bride and at the centre of them all, in pride of place, a large studio portrait of two beaming toddlers.

"My wife and daughter; our two grandsons." He didn't elaborate any further and, taking in the rest of the room, nowhere could Elizabeth see a picture of John. Tucking her skirt underneath her, she took a seat on the couch as he lowered himself into what was obviously his armchair; a pair of reading glasses and a neatly folded newspaper lay on the small table next to him.

"So, are you here to tell me my son is dead?" The question was asked without trace of emotion and Elizabeth found her self taken aback by the matter of fact manner in which he'd asked it. "Don't look so shocked, Doctor. I know my son and it's always been a matter of when rather than if he'd get himself killed."

"I'm here to inform you that John is MIA, Colonel, but we have every reason to believe he is still alive."

"You believe he's been captured?"

"Yes, unfortunately we don't know by whom or where exactly he is being held."

"Is he out in Iraq? Because if Iraqi militants have got hold of a American pilot then…" His voice wavered for a moment, just the trace of emotion, before he recovered. "Then the only time we're going to see him again is when they post his beheading on the internet." It was strange, and she found herself feeling ashamed of the fact, but the reality of what was happening on Earth had become diluted for her. She spent her time dealing with matters on an intergalactic scale, it was easy to forget the very real dangers that people were facing on Earth.

"I'm afraid the location of our base of operations is highly classified information, as is the specifics of our mission; but I can tell you that we are not working within the Middle East."

"Highly classified?" He raised an eyebrow. "Is there anything you can tell me?" Leaning forward, she entwined her hands and rested them on her knees.

"Very little, only that our mission is of great importance on an international scale."

"Hmm." He seemed to consider this for a moment. "And what exactly is your role in this 'mission', doctor?"

"I am the head of our project."

"You're a civilian." It sounded more like an accusation than a statement of fact. "May I ask what exactly you're a doctor of?"

"International relations."

"International relations." There was an element of disdain in his voice and a mocking smile on his face. "So, Doctor Weir, why is the head of such an 'important' classified operation going to the trouble of personally informing the family of a missing pilot?"

"I'm not. I'm personally informing the family of my military CO." Tom Sheppard spat out a laugh and shook his head.

"What kind of half-assed set up are you running if that you'd put a screw up Major in charge?"

Elizabeth bit her tongue, keeping her composed tone of voice.

"Actually he's a Lieutenant Colonel these days and a highly regarded one, I might add." She felt some satisfaction at his reaction; it was something he hadn't been expecting and it had put a crack in his mask, letting a hint of his uncertainty back out. "I really don't know what we would have done without him these past couple of years, he has acted above and beyond the call of duty, showed incredible courage and selflessness; proved himself time and time again."

"He always could charm the women." Elizabeth drew in a sharp breath, this time she didn't bite her tongue.

"Well, he clearly didn't get that from you." Silently she berated herself for snapping at him but couldn't help noticing the comment had made him sit up a little straighter. "Colonel, I don't know what happened between you and your son but John is one of the best men I have ever known and if you are so determined to hate him that you're going to twist everything I say, that you have to make sordid insinuations about me simply because I have a high opinion of him, then I feel sorry for you." Standing, she picked up her suitcase and stepped toward the hall. "I don't see any reason for me to stay any longer, do you?" Stopping for a moment, she turned back. "You know, when you first opened the door I was taken aback by how much alike the two of you are but the similarity is clearly only skin deep, because I find myself unable to picture John being so utterly heartless."

"Heartless?" The Colonel rose to his feet, his face flushed with anger. "John has hurt everyone who has ever cared about him; he's just a selfish, irresponsible kid. You think you know him but you don't, he's reckless and dangerous, it's like he's got a built-in self destruct mechanism. Every time I thought he'd pulled himself together he'd go and do something stupid. Maybe it would be better for everyone if he was dead." Tom Sheppard stopped abruptly and stood looking shell shocked, confusion on his face as he processed what he'd just said, but Elizabeth had a hard time finding sympathy for him.

"I can see my coming here was a mistake, Colonel. I can only hope that when our mission finally becomes public knowledge you'll realise how mistaken you are and you'll be proud of him, because God knows I am."

As she slammed the front door behind her and marched back up the street she felt like screaming. Anger boiled inside her, anger at herself for getting mad with him, anger at him for being so bitter and twisted, anger at John for putting her in this position in the first place.

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_A/N As I'm sure you've realised, this chapter is allows for a bit of a time jump. I hope you can all forgive me for that, but the alternative would have been several very dull chapters.  
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	4. A Place Called Home

**Chapter 3**

**A Place Called Home**

Weeks must have passed since he woke up, surprised and vaguely annoyed to find himself still alive, but how many, he couldn't tell. Time didn't mean anything to him anymore, the bastards had taken his watch, and here there were no days or nights, just walled in darkness; some days he felt like he had always been here and that his memories were just fantasies. No one ever opened the door, no one ever spoke to him; if it wasn't for the food that was occasionally pushed through the slot at the bottom of the door, he would have thought they had forgotten about him, or that the universe outside had simply ceased to exist.

They had taken his clothes too and replaced them with a thin shirt and trousers, leaving him bare foot. They had taken his dog tags, they had taken everything that identified him as being John, except one thing; they had left his sweatband. He didn't know why but it was still there on his wrist, tattered, bloody, but still there. It seemed silly that such a small thing could hold so much meaning for him but it was like a lifeline to the real world, the life he had before; before the world had consisted of these four walls. It was proof that he really was John Sheppard.

ooOoo

Eighteen days on the Daedalus felt like a year; she really didn't know how Caldwell and his crew stopped themselves going crazy. There was little in the way of paper work to do until she got back to the city, when she knew she'd be overwhelmed with it, and so she had found herself wandering aimlessly around the ship, trying to find something to keep herself occupied. She'd heard the life stories of half the Daedalus crew; bored with each other's company, they seemed relieved to have a new audience for their stories and anecdotes, some had proved to be talented narrators, others had proved mind-numbingly dull.

Colonel Caldwell had challenged her to games of chess or backgammon when he was off duty and she had even spent time with Hermiod who, she was surprised to discover, was actually something of a gossip. When she needed time to herself, she sat and reviewed the mission reports from the SGC detailing the ongoing conflict with the Ori. So far they were unaware of the existence of the Pegasus Galaxy but they had to be prepared for any eventuality.

This wouldn't be Steven Caldwell's last return trip to Atlantis with the Daedalus, he was still technically the ship's commander and would remain so until his next return to Earth, when it had been agreed that he would be officially confirmed as the military commander of Atlantis. Elizabeth hadn't challenged the decision, in fact she supported it; in the time she had known him she had gained a great deal of respect for the Colonel and, the better she got to know him, the more she valued his input. He was a good man and he would do his best for Atlantis and she could ask no more than that.

As soon as they had begun the approach to the Atlantean planet, she had gone to the bridge to watch. Standing up close to the panoramic window of the bridge, it almost felt like she was flying down through the atmosphere and across the wide expanse of ocean and then, rising up out of the water like a magical citadel from a fairytale, there was Atlantis. Her heart swelled with pride and joy at the sight of the city, her city; she was home.

ooOoo

Stepping out of the Daedalus and pausing to breathe in the cool sea air, she realised just how much she had missed Atlantis. The gentle breeze encircling her felt almost like an embrace, gently blowing her dark curls around her face. As she stood drinking in the moment, she heard Rodney's voice above the bustle of the crew disembarking the ship. The tide of people were going against him.

"Excuse me! Excuse me! Important person trying to get through here." The crew continued to jostle past him. "What? Am I talking to myself?" She laughed gently under her breath; yes, it was definitely good to be home.

"Rodney, good to see you." Stumbling through the last wave of people and straightening himself up, he smiled at her, a softer version of that familiar self important expression.

"You too. How was Earth?"

"Oh you know, still there. How about Atlantis? I hope you haven't blown up anything too important while I've been gone." He narrowed his eyes at her, and she looked back in mock innocence, her eyebrows slightly raised and a playful smile on her lips.

"It's nice to know you have such faith in me. A guy blows up five sixths of a solar system one time and he's never allowed to forget it."

"Well, we have to remind you you're not perfect sometimes. So really, what have I missed? Any trouble?"

"A little. Lorne's team had a run in with some Wraith a couple of weeks ago but nothing they couldn't handle." He dismissed the incident with a wave of his hand before a more serious expression took over. "Edison's team had a close call though; ran into some less than friendly locals. Granger was shot twice in the leg but Beckett tells me he's making a good recovery."

"Do we know anything about the people who attacked them?"

"Not really, we were told they were traders but if that's the case they need to work on their customer service."

Elizabeth furrowed her brow. "What else?"

"Well, the exploration of the central western section of the city is going well; we've discovered what we think was a school room, the linguists and anthropologists are having a field day translating children's stories."

"I bet, I wouldn't mind a look myself."

"Each to her own, all seems rather pointless to me." She shook her head. "Well, it does. What are we going to learn from the Ancient equivalent of Little Red Riding Hood?"

"You can learn a great deal about a culture from the stories they tell their children." He didn't look convinced and she knew she'd never be able to persuade him, so she changed the subject. "Anything else I should know?"

"Not really. Oh, there is one thing, Dr Kavanaugh is currently in the infirmary with a concussion." Rodney's blue eyes shone with amusement and a smug smile appeared on his face.

"What happened?"

"I thought it might do him good to pay a visit to the kids on M7G-677. Unfortunately they got a little too…playful…with him." Elizabeth caught herself laughing.

"That's not funny."

"Oh, I don't know, it kinda is." Smirking, he fell into a leisurely pace beside her as they wandered into the city.

"Nothing else. No…news?" She already knew the answer but couldn't help herself asking and felt guilty when she saw his shoulders visibly slump.

"No." They walked in silence for a while, each of them lost in thought. She knew he blamed himself, even though no one else did, but she also knew there was nothing she could say to make him believe otherwise.

When finally he did speak again his upbeat tone of voice sounded forced. "Well, some of us have work to do." He reached out and patted her arm awkwardly, showing affection was not something he was particularly good at, which to Elizabeth made the gesture all the more touching. "Good to have you home."

"Thank you, Rodney. It's good to be back."

ooOoo

It had become something of a ritual; when he heard their footsteps coming to bring him food he would lay flat on the floor, his head on one side against the cold stone, so he could see through the gap that the tray would be pushed through. All he ever saw was a hand place down the tray and a booted foot push it through. The only real comfort he got from this was the fact that it was a human hand - the way he saw it that had to be a bonus. To begin with he had called out to them, at first wisecracks but that had soon degenerated to screaming abuse and eventually just begging for them to say a word, to say anything, even just to tell him to shut up. It felt like a lifetime since he had heard another voice; now he rarely made the effort.

Opposite his cell he could see another one but that stood empty. He had watched for hours in the hope of seeing movement but he never did and the guard never left food there. The footsteps echoed down the corridor - at least in his mind he imagined it being a corridor, in truth he didn't know what was beyond the door, had never even seen the faces of his captors. The boots stopped outside the door, boots so shiny they could only belong to a soldier, and a hand came into view, setting down the tray. A long scar ran across the palm of the hand; this was his usual guard. The hand retracted and the tray was kicked through. He watched as the feet disappeared, heavy footfalls moving away from him, the tiny piece of human contact he clung to had passed for another day.

Pushing himself up into a sitting position, he reached out and dragged the tray toward him. He looked at the dark stew in the bowl and the grey flatbread. The first time he'd eaten it he'd retched but he'd soon discovered the easiest way was to swallow it quickly, not giving himself time to taste it, and to never try and work out what was in it.

ooOoo

It had taken her half an hour to get back to her quarters, being stopped by at least a dozen people on the way. Teyla and Carson were waiting near the transporter and she had hugged them both, thinking that it was strange that it had taken something like this to strengthen their friendships.

Carson had his mother hen face on, worried that she would go straight to her office and throw herself into work again, especially when she insisted on accompanying him to the infirmary to check on Granger's progress, but, after seeing the sergeant for herself, she assured him that she intended to go straight to her quarters, shower, and then sleep for at least ten hours. He didn't look convinced but at least he stopped nagging.

Even Ronon had made the effort to see her, though he claimed that his presence in the corridor between the transporter and her quarters was purely coincidental and that he had forgotten she was returning so soon. She knew in his own way he was checking up on her and letting her know he was still around.

Once she finally got through the door, and it had closed behind her, she dropped her bags on the floor and slumped down on the bed, exhausted. She needed a good night's sleep. Somehow she never quite managed that on the Daedalus. Most of the unpacking could wait until the morning, she decided, and reaching down, she unzipped one of the bags and pulled out a couple of paperback novels she'd bought herself. Pure fluff of course, and she'd never admit to reading them, but she was entitled to her guilty pleasures the same as everyone else.

Opening the cover of one of them, she took out the envelope that had arrived at the SGC two days before she departed. Opening it, she found herself smiling again; John looked back at her from the photograph, baby faced and floppy haired, but still undeniably John, that same lazy grin, the same hint of mischief in his eyes. Turning it over she looked at the message John's father had written on the back.

'_We don't leave people behind_.'


	5. Getting Back On The Horse

_A/N Finally I'm actually able to read my reviews and thank you all for being so positive, I just hope I don't go on to disappoint. The only thing I can say to those of you who are worried about poor, sweet Shep is that there's a lot more of this story to come, hopefully over the course of the next few chapters you'll have a better idea of where I'm heading because right now I'm only just getting started.  
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**Chapter 4**

**Getting Back On The Horse**

Rodney McKay hadn't left Atlantis while Elizabeth had been on Earth. He'd done his best to fill her shoes during her absence and but he lacked her people skills. He knew that everyone else was relieved when she returned and so was he. Having to spend time on the mundane tasks that running a city involved had made him even more irritable than usual and being torn away from the lab so often was frustrating to say the least. He'd got a long list of projects waiting for him and having to let Zelenka take charge over certain areas that he considered his domain had really riled him.

Besides, he'd missed her. She was a comforting presence and one of the few people he knew he could truly call a friend. Now she had been back for a couple of days and he would be able to return to off-world missions. He knew this was why Elizabeth had called him to her office this morning and his heart sank at the prospect. How could he possibly face going back out there? He took a deep breath before walking into her office. Ronan and Teyla were already there with one of the new marines who he had a vague recollection of being introduced to a couple of days before.

"Rodney," Elizabeth got up as he came in and walked around the table. "Come in." She put out her arm, ushering him toward the woman seated on the couch; she got up as Rodney approached. "You've met Captain Frischmann?" So that was her name?

"Er…yes. Briefly." Frischmann smiled at him.

"Dr McKay was rather busy at the time. We'll try the introduction again, shall we?" She stuck out her hand. "Captain Isabella Frischmann. Pleased to meet you, Doctor." She was about the same height as he was and her blonde hair was cropped short. When he took her hand to shake it she nearly crushed his fingers.

"Likewise. So, can I assume you'll be working with us?" Elizabeth answered his question for her.

"Well, as you know, we always put new recruits with experienced teams to begin with and, seeing as the three of you are currently without a military officer, Colonel Caldwell and myself felt that Captain Frischmann would be the ideal candidate to join you."

"Of course. " Rodney nodded. Of course, he'd known it was only a matter of time before Sheppard was replaced but he hadn't quite prepared himself for the reality of it. There was a moment's awkward silence. Elizabeth moved back toward her desk, picking up a PDA.

"Teyla seems to think that this planet may hold something of interest for us."

"You remember my friend, Feara? Well, she has been trading with this world for many years and a local told her a story about what sounds like a possible Ancient structure." Teyla explained.

Elizabeth handed the PDA to the scientist. "We've had a team do a fly over and there's something there, the geography is going to make it difficult to get a jumper in so you'll have to go in on foot. But it's only a couple of kilometres from the gate." Rodney groaned. "The exercise will do you good, you've been sitting behind a desk for the last few weeks. " She teased. "So?" She tipped her head to one side and looked at him encouragingly. "Wanna go take a look?"

ooOoo

And that's how, the next morning, Rodney found himself standing in the gate room, kitted up, his sidearm strapped to his thigh. He stood fidgeting, making sure he had all of his equipment in his backpack.

All Rodney wanted was to get this mission over and done with. Normally, he'd be excited at the prospect of finding something new but today he wasn't in the mood. Besides, even if he did find something cool, who was there to get excited about it with him? Teyla would do her best, and Ronon might raise an eyebrow if it was something impressive but they wouldn't be able to keep up with him like Sheppard could, they wouldn't really understand.

"Ready to go, Doctor?" He looked up. Captain Frischmann smiled back at him, clearly eager to get going. From the little time he had spent talking to her, she seemed pleasant enough, and she was obviously trying to be sensitive to the situation, but she didn't belong and he couldn't pretend otherwise.

"Yes. I think I've got everything." He stood up straight, swinging the backpack up on to his shoulder.

"Okay then." She spoke into her earpiece. "We're ready to go, Doctor Weir." McKay looked up to the control room. Dr Weir and Colonel Caldwell stood side by side on the balcony outside her office. Elizabeth nodded at the gate technician who began the dialling sequence. As the wormhole burst out into the gate room, she looked down at Rodney and raised her hand in a small wave. He forced a smile and returned the gesture before stepping through the event horizon.

ooOoo

_Pushing the door open gently, he saw her sat in her chair, silhouetted against the window, her head tilted away from him as if she was studying the horizon. The warm evening sun streamed in through the glass, picking out gold glints in her long hair. He crept quietly into the room, not wanting to disturb her if she was sleeping but needing to be near her; as he moved closer she didn't stir. Seeing that her blanket had fallen to the ground, he reached down to pick it up and place it across her lap. _

_As he stood up, he noticed her withered hand resting on the arm of the chair, dry and claw-like. His eyes snapped up to her face; dead eyes stared back, her cheeks sunken, lips drawn back over her teeth and, at the neck of her nightgown, the red handprint of a Wraith. Dropping the blanket, he turned to run, screaming as loud as he could, but the door had blown shut and he couldn't open it. He shook the door, sobbing and screaming…_

Waking up was a battle, the nightmare not wanting to let go; he realised that he was still calling out for his father in shallow little gasps, his face wet with tears. He had been seven years old when he had found his mother dead in her room. The doctors had said she would have a couple more months, as far as his young mind was concerned they had lied. In reality, she had looked peaceful in death but the nightmares had robbed him of that, all his mind did now was torment him. The night she died he sobbed in his fathers arms until he fell asleep. When he woke the next morning his father was still there, holding on to him as if he was scared to let go.

ooOoo

The rain was cold and, no matter how he adjusted his uniform, it seemed to find a way down Rodney's neck. The local area consisted of a vast, evergreen forest covering rocky slopes that undulated in gentle rolling hills, leaving dips and valleys. The path they walked along wound through one of these little valleys and the water ran down from either side of them until they were up to their ankles in thick yellow mud. They headed toward the village; they had planned to check in with the locals anyway but now they also hoped for somewhere to dry off and get warm, hopefully until the rainstorm passed. They could see the little settlement on a hill up ahead of them. Rodney had suggested that they get to higher ground but the slopes around them had become slick with water and would have been dangerous to climb, so they kept plodding on.

"I'm going to be in bed for a month after this. I'll catch pneumonia, or hypothermia. My body is very sensitive to temperature change."

"Yes, Rodney." Teyla bit her tongue. "That is why we must move quickly. Once we get to the village we will find warmth and hospitality, I am sure."

The shot rang out just as Teyla finished the sentence. They dived for cover, McKay feeling Ronon's hand grab his vest and drag him with them, pushing him face down into the mud at the base of one of the slopes. He raised his head, looking for a part of his hand or arm that was free of mud so he could wipe his face but, realising he was saturated in the stuff, gave up. A second shot rang out, a little too close for comfort.

"Somebody's shooting at us!" McKay fumbled to get his gun out of its holster.

"We'd noticed," the Captain snapped back, unable to hide her annoyance.

"Over there." Teyla gestured and through the grey veil of rain Frischmann and Ronon spotted the marksman on a rocky outcrop on the opposite slope; a second assailant could be seen moving in the scrub at the base of the rise.

"I can see two of them, are there any others? McKay?"

"Um…" He pulled the scanner from his backpack. "…Over there - they're moving around to the east of us, three of them heading this way through the trees. They're moving fast."

"We can take them easy." Ronon nodded his head in the direction of the two snipers across the narrow valley. "Those two are mine." Jumping up, he ran from their hiding place, firing as he went. The captain looked after him and cursed loudly, an angry look on her face.

Ronan zigzagged between cover toward the sniper and his companion. For a moment McKay thought Frischmann was going after him but the other three dots on the screen were getting closer. Rodney called out to her just as the first shots were fired from behind them. She turned around, immediately raising her weapon and opening fire.

He didn't look to see what she was shooting at but dived for cover behind a boulder, his hands over his head. A few seconds later Frischmann dropped down beside him.

Chancing a glance around the side of the boulder, he could see the bodies of two of their adversaries lying sprawled on the ground where Frischmann's bullets had cut them down, patches of scarlet blood soaking through their pale grey uniforms. He looked for Teyla but could see no sign of her; glancing at the captain he could see she was wondering were the Athosian was too. He heard Frischmann swear quietly under her breath. The only noise beyond their own breathing was the dull report of Ronon's gun on the other side of the valley and then that stopped too.

They crouched there for what seemed like an eternity, time stretching out, both of them tensed, pushing their senses to the absolute limit, waiting for the attack. Suddenly there was movement to the right of them; the captain swung around, pushing McKay behind her as a bullet whipped past. She raised her P-90 but, just as she did so, Teyla appeared behind the gunman. The Athosian slammed her elbow into the mans spine, swinging out her leg to bring him down to the ground, whilst at the same time disarming him and slamming the butt of his own rifle into his head. By the time he hit the ground, both Teyla and Frischmann had their guns trained on him.

"Teyla, I think there's one more."

"There was but I have dealt with him."

"Well, let's hope that's all of them." She surveyed the trees. "Where the hell is Ronon?"

"I'm here." The Satedan walked calmly toward them. Frischmann looked at him, clearly still annoyed, then she turned to McKay who was crouched down, bending over the scanner in his hand.

"I'm not picking up anymore life signs."

"Yeah? Well that thing didn't work so well, McKay. You said there were only three this side, I counted four." He looked up at her.

"Well they must have been standing too close together or something. I can barely see a damn thing in this weather anyway," he snapped back before noticing the change in her expression, from annoyance to concern.

"Are you hurt?"

"What? No, I don't think so. Why? Do I look hurt?" She gestured to his head; he put his muddy hand up to his forehead and brought it back down, staring at the blood on his fingers mingling with the yellow mud. "Oh my God! I'm hurt!" His eyes opened wide. "We have to go, I need a doctor." He scrambled up and, in his panic, slipped in the mud, landing with a splat. "You see? I'm weak from blood loss." She reached down to help him up.

"Take some deep breaths Doctor, and let me take a look." He looked at her suspiciously but allowed her to examine his wound. Smiling, she let out a small, relieved chuckle. He pulled away, glaring at her in indignation.

"I hardly think this is a laughing matter, Captain."

"No, it's not Doctor, but you are a very lucky man."

"Lucky?"

"Yes, lucky. A little bit to the left and that bullet would have gone through your head instead of just grazing it." It took a moment for this information to sink in. He stood with his mouth opening and closing before putting his hand up to his head again.

"Oh my God! I've been shot!" There was a collective groan from the others but, as he glanced down at the scanner still in his hand, his injury was forgotten. He wiped the mud from the screen as best he could and through the smears saw the screen was lit up with dots. "Oh crap!" He turned the screen to face the others. "We really need to go…now."


	6. Pressure Point

_A/N: More positive reviews, thank you all so much but please feel free to offer criticism too. _

_It's strange, I have pretty much this entire story written in first draft form, so it's only looking at it chapter by chapter as you guys are seeing it that I realise how little Shep there is in some chapters, sorry about that. I'm afraid this is another Shep-lite offering but I promise you'll start to see a little more of him as the story progresses. _

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**Chapter 5**

**Pressure Point**

When the gate activated, Elizabeth and Colonel Caldwell stood watching the shimmering wormhole. Frischmann's voice came across the radio.

"We're coming in hot, under heavy enemy fire." She sounded out of breath and, in the background, gunshots could be heard. Elizabeth gripped the railing tighter and willed them all to come through in one piece. Teyla was the first one through, closely followed by a bullet that ricocheted off the steps leading down to the gate. Everyone ducked, an involuntary movement. Seconds later, Frischmann came flying through the gate backwards, P-90 still raised, and then finally Ronon, half carrying an exhausted looking Rodney and shooting backwards through the gate as he came. All four of them were caked in thick yellowish mud and their feet slipped on the smooth floor of the gate room.

"Shield up!" Elizabeth called out as she ran down the steps to greet them. "And get a medical team down here now!" She immediately noticed the blood on Rodney's head and grabbed hold of him. "Are you okay?" He managed a weak nod which slowly turned into a shake of the head.

"I've had better days," he panted, pointing at the wound on his head. "I got shot."

"McKay, it's just a scratch." Ronon said impatiently as he sat on the floor pulling off his water-logged boots. Frischmann stood with her hands resting on her knees and her head down, trying to catch her breath. Teyla removed her water-logged vest which fell with a slap, splattering mud across the floor.

Caldwell stepped up beside Elizabeth.

"You all okay?"

"I think so, sir," Frischmann said, looking around at the others. "We're damned lucky though."

"What the hell happened?"

"We do not know." Teyla answered. "We were attacked without warning."

"By the locals?"

"I do not believe so, Colonel. They are simple farmers, they do not possess weaponry anywhere near this advanced."

"I seem to recall that we thought the Genii were simple farmers too." Teyla dropped her eyes from him, a mixture of sadness and guilt in her expression.

"That's enough for now, Colonel." Elizabeth turned to see the medical team enter the gate room. "Carson, I want all of them given a through check up."

"Aye. No worries."

"And you are all off duty until Doctor Beckett says otherwise." She smiled lightly at them, relieved to know that they were all going to be okay. "Or at least until you've had a good shower."

ooOoo

The next morning Elizabeth wandered into the mess hall. She glanced around and spotted Teyla and Carson sitting in one corner. Grabbing a cup of coffee, she decided to treat herself to a pastry before walking over to join them. Carson welcomed her with a cheerful "Good morning" and Teyla shifted over slightly to let her sit down, a warm smile on her face.

"Good morning you two. How are you, Teyla?"

"I am well, thank you."

"Nice to see you taking time for breakfast." Carson was never fully off duty.

"Yes, mom." She deadpanned, before throwing the medic a mischievous grin. "Really Carson, I'm fine, I've been eating." He looked at her doubtfully. "I've just been taking meals in my office, I have had a lot work to catch up on."

"I thought as much. Well, you should make some time to catch up with your friends as well as your work."

"Well, that's what I'm doing now isn't it?"

"Then I guess you're forgiven…for now."

"Carson is correct, we have not really had time to talk to you since your return." Teyla added. "How was your visit to Earth?"

"Lots of very boring debriefings and reviews. I sometimes think my life is turning in to one big meeting."

"And a mountain of paper work." Carson added with a sigh that said he knew exactly how she felt.

"One of the benefits of being a warrior is the lack of paperwork." Teyla looked at them with a happy smile.

"You just make more for the rest of us." Elizabeth berated jokingly.

"Exactly," agreed the doctor, much to Teyla's amusement.

ooOoo

It was four steps from wall to wall, he'd walked back and forth 529 times that was 2,116 steps, the square root of 2,116 was 46, 2,116 times 46 was 97,336. He kicked out at the wall in frustration, momentarily forgetting that he was barefoot.

"Damn it." Slumping down on his mattress, he rubbed his foot before pulling the grubby blanket around his shoulders. How long, he wondered, was it before stir crazy turned into just plain crazy? Keeping his mind occupied was becoming ever more difficult; he couldn't even count the damn bricks because there were no bricks, just smooth walls. Not smooth like Atlantis but hard, cold rock. _Atlantis_. Caldwell would be in charge now. He found that a strangely comforting thought; the Colonel was a good man, he'd do his best for them. Do his best for who? Who was still alive? Who was dead? _Maybe they're all dead. _He hugged the blanket tighter around him. Maybe he was never getting out of here, maybe the reason they no longer interrogated him was because they didn't need him anymore because everyone was dead. Beckett and Caldwell, Zelenka, Lorne, all of them.

But if they were dead, why wasn't he? What was the point? There was no point. Nothing had a point anymore. No night or day, no purpose, no future, no past, just a dark little box and a dirty mattress. Death had followed him all his life, taken the people he loved and tainted his hands with blood, this was why you didn't let people get close because then you cared and if you cared it ripped you apart when they went away. But he'd let people in without ever really meaning to and now he was being punished for it.

ooOoo

"I went to see John's father." Her voice was quieter now. The atmosphere at the table shifted and Elizabeth hated the fact that the mention of his name immediately caused tension. Teyla and Carson's reaction was unconscious, but still she felt it. She found herself thinking how nice it would be for the wounds to be sufficiently healed for them to be able to talk of him and remember the good times rather than his loss. Though every time she found herself having such thoughts she admonished herself for giving up on him.

"It is strange, I do not remember John ever speaking of his family."

"No lass, can't say I do either."

"Well things aren't so good between John and his father. I didn't realise just how bad they were though. I have to say it wasn't the most comfortable experience of my life; to tell the truth it was awful, we ended up practically shouting at one another. There's a lot of bitterness there but then just before I left Earth I got a letter from him. It didn't say much, just an apology really, but I think it shows there's still love there. This photograph was in it." She pulled it out and passed it to Carson who let out a chuckle.

"Good grief. How did they ever let him into the air force with hair like that?" He passed the picture to Teyla. As she looked at the image a smile lit up her face.

"So young!"

"Who?" Rodney and Ronon put their trays down on the table, causing the others to shift over and squash their own crockery up to make room. The two of them appeared to have cleaned out the kitchens, both of their trays stacked up with assorted breakfast foods. They had barely sat down before Ronon was stuffing the food in to his mouth with his hands. Rodney, who wore a large white bandage across his temple, took a bite of his toast and a slurp of coffee before repeating the question.

Teyla passed him the photograph and, putting down his food, he took it.

"Huh…" If Sheppard had been there he would have delighted in making him squirm at the ridiculous pretty boy hair but right now he didn't want to look at the picture a moment longer than necessary; he handed it over to Ronon. As the Satedan turned it round, Rodney caught sight of the hand written note on the back. His stomach knotted and suddenly the thought of food made him feel sick. They'd left him behind.

"I'm sorry, I have things to do."

Getting to his feet, he hurried out of the refectory and down the corridors toward the lab, immediately regretting the loss of his coffee, angry at himself for running out of the room like a child; once again he'd made a fool of himself. When he reached the lab he was glad to see it empty. Throwing his jacket across the back of a chair, he opened the laptop and started bringing up the calculations he had been working on, losing himself in the figures on the screen.

Only a few moments had passed when a cup of coffee and a Danish were set down on the bench beside him. He closed his eyes and sighed, knowing someone had come after him. He looked up expecting to see Elizabeth or Carson, maybe Teyla, what he didn't expect to see was Captain Frischmann standing beside him, blowing gently on her own coffee. Taking a sip, she smiled at him.

"You looked like you could do with some caffeine and sugar."

"Um…yes." He looked at her, slightly confused and more than a little suspicious. "Thank you." He picked up his own coffee. "Much appreciated. Now was there something I can do for you?" Right now he really didn't want any company.

"Not particularly, I was just wondering how your head was."

"What?" He'd almost forgotten about the graze on his temple. "Oh, fine. It's healing up nicely. Now if you'll excuse me, I have work to do." Turning back to his laptop, he resumed studying his calculations.

"Whatcha doin'?" Closing his eyes, he counted to five.

"It's really very difficult to explain in layman's terms. I doubt you'd understand the complexities of it."

"Yeah, you're probably right." He nodded, once more turning his back to her and studying the screen. After a few seconds, he realised she was still standing behind him. Turning, he glared at her; she smiled back, "Oh, don't mind me. Carry on."

"I can't work if you're going to stand there looking over my shoulder. Don't you have soldiery things to go and do?"

"Not right now, we've all been told to take it easy today, remember?"

"So you thought you'd just come here and annoy me instead?"

"No. I just saw you making your escape from the mess hall, you looked upset, and I thought you could do with some company, even if you don't realise it." He looked at her in surprise, unsure what to say. "Look, I know you don't want me on the team but, for the time being at least, you're stuck with me, so we might as well try and get along."

"It's not that I have anything against you..."

"No, you just miss your friend." It was a simple statement of fact, but it hit home. McKay looked at the desk, the laptop, anywhere but at her. "It's normal you know, it doesn't make you weak, it isn't going to make anyone think any less of you, in fact it might make a few people realise you're human after all. And if everything I've heard about Colonel Sheppard is true, he would kick your ass for sitting here feeling sorry for yourself." With that she headed for the door, only pausing to say. "Enjoy your coffee, Doctor."

"Captain!" She kept walking. "Izzy?"

Leaning back around the door, she raised her eyebrows. "Yeah?" He swallowed hard, unused to making apologies, but knowing she deserved one.

"I'm sorry I snapped at you."

"Ah, you're okay. Geniuses are supposed to be cranky right? It's in the job description." And with a smile she left him to his own thoughts.

ooOoo

"Do you think one of us should have gone after him?" Elizabeth asked Carson.

"I don't know, lass. He's got to talk to someone sooner or later but we can't push him; you know Rodney, he'll just clam up even tighter. I've tried talking to him, Kate too, but he's just not ready yet."

"He blames himself." Ronon stated. "But I am every bit as guilty as he is."

"Ronan, that's nonsense lad and you know it."

"Carson's right, what happened was no-one's…" at that moment Elizabeth's earpiece activated, the message: "Unscheduled off world activation!"

Elizabeth ran to the gate room, Teyla and Ronon in tow. Colonel Caldwell stood beside the gate technician; he turned as he saw her.

"It's Ripley's team, they're coming in hot." A voice came over the radio but it wasn't Lieutenant Ripley.

"Ouvrez le bouclier! Nous sommes attaqués!" With the shield down, a shot came through the gate, causing everyone in the control room to duck. Etienne Lepreux ran through the gate, not stopping until he had reached Elizabeth. He clung to her arm, gasping for breath, a look of sheer terror in his eyes. They turned back to watch the gate but no one else came through. Caldwell tried to contact Ripley via radio but got no reply. A couple more shots came through the gate. Meanwhile, the French scientist continued to ramble incoherently. Elizabeth grabbed him by the shoulders and looked him straight in the eye.

"Qu'est-ce que s'est produit?" He looked at her in despair.

"Ils sont morts, ils sont tous morts." _They are dead, they are all dead._


	7. Breaking Point

_A/N Thank you once again for the reviews, please keep them coming. I know this story may seem quite slow in developing at the moment but I promise that in the next few chapters things will start to move pretty quickly_. _Honest!_

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**Chapter 6**

**Breaking Point**

Laying in his usual spot, waiting for his food, he focused on the old tray he had pushed back out into the corridor. The copper coloured bodies of tiny bugs flittered across its surface; the arrival of the guard caused them to open their wings and drift away. A new tray was pushed through and he shoved it back, slopping the stew over the guard's shiny boots, and was rewarded with a curse from the guard. It was barely a murmur under his breath but, to John, it felt like a tiny victory. He'd tried waiting them out but he was beginning to doubt his own sanity and had decided to renew his efforts to get a reaction from the guard.

The guard sighed and pushed the tray back through; again he rejected it, hoping that this time the man would speak to him but, once again, the tray was nudged back through. Infuriated, Sheppard got to his feet and kicked the tray. The bowl rolled off so he kicked that too, the metal rim bruising his bare feet, but that only served to feed his anger; he kept kicking out at the door, then he punched it, screaming at the top of his lungs until his throat felt raw. Taking a step backward, he flung himself shoulder first at the door; he punched and tore at it, repeatedly hurling himself at it. His knuckles were raw and bloody and could feel the dull throb of bruises developing across his skin but he still didn't stop, he couldn't stop.

"Bastard!" He could sense that the guard was still there. "Do something, say something, ANYTHING!" He continued to attack the door, the pain comforting, because at least he could feel something other than the dull emptiness that was consuming him. "C'mon you son of a bitch, talk to me!" He punctuated each word with a kick or punch. Footsteps echoed away from him. "NO!" Panicking, he got down on the floor and looked out into the corridor. "No! Don't leave me. Bastards! BASTARDS!" Suddenly a pair of boots appeared outside the door followed by a second pair slightly behind them, causing him to jump back from the door, scuttling across the floor and pushing himself up against the wall.

"Can we not just kill him?"

A sigh. "If it were up to me we would have been rid of him long before now but we must follow orders." It was the same voice that had told him what had happened to Elizabeth and his team; the same calm, storyteller tones. Stunned into silence, he got to his feet and stood facing the door, his back pressed against the wall, breathing heavily, a sick feeling rising in his stomach, equal parts excitement and dread.

ooOoo

Twenty minutes after Ettiene Lepreux had come through the gate, Elizabeth stood in the infirmary waiting while Carson gave orders to a nurse once he had finished he came over to join her.

"How is he, Carson?"

"In shock, I've given him a sedative. Poor man's been through hell." He looked back to the man now dozing gently on the bed. "He's only been here a couple of months, never been in a hostile situation before." Colonel Caldwell entered the infirmary and walked over to join them.

"We've just brought the MALP back. It's reading no life signs in the immediate vicinity now and the video feed shows at least two bodies in the area surrounding the gate." Elizabeth closed her eyes and let out a long shuddering sigh. In her mind she pictured the faces of the six young men and women who had stepped through the gate just a day before on a routine mission. "With your permission, I'd like to send a team in to retrieve them."

"Yes, of course, Colonel. Just be careful, straight in straight out. They stay close to the gate. I'm not losing anyone else today. I know they want to bring everyone home but if the bodies aren't in the immediate vicinity of the gate, they are not to go looking for them. Not until we know it's safe."

"Don't worry, I'm not going to let them take any risks." He turned to Carson, nodding in the direction of the French scientist. "How is he?"

"He's in severe shock. I'm afraid you won't be able to talk to him again until the morning at the earliest." The soldier turned to Elizabeth.

"Did you manage to get anything out of him at all?"

"A little. He was pretty incoherent but I think I've managed to piece it together. They were ambushed on the outskirts of the village. From what he said, they were vastly outnumbered. Lt. Ripley tried to get the scientists back to the gate but…" She trailed off.

"And we don't think this was the locals?"

"No. We've been trading with them since we first came here, we've always had a good relationship with them."

"Aye, I've been there myself on several occasions, Colonel and they're a peaceful people."

"Not to mention the fact that they don't have weaponry anywhere near this advanced." As the words left her lips Elizabeth realised she had heard them spoken only a day before. Elizabeth sighed inwardly; she had been so caught up in what had happened and dealing with Dr Lepreux that she had not made the possible connection between this attack and the one on McKay's team. The Colonel voiced her fear.

"That's two teams attacked by an unknown military force in the space of two days, it's too much of a coincidence for my liking."

"What about Edison's team?" The two leaders looked sharply at the doctor and he continued, nervously. "Well, as far as I'm aware, we haven't discovered who the people who attacked Edison's team last week were. At the time we just assumed they were unfriendly locals. But Sergeant Granger was shot in the leg and not many races we've come across are well enough advanced to have developed guns."

"Damn it." Caldwell snorted. "Do you still have the bullet you took out of Granger?"

"Yes, of course."

"A shot came through the gate just before Doctor Lepreux." The Colonel nodded toward the man in the bed. "We'll compare the two see if we're looking at he same kind of weapons."

"Good idea. In the mean time, how many teams do we have off world?" Elizabeth asked

"Four."

"Recall them as soon as possible, and suspend all non-essential gate activity until we get a better idea of what the hell is going on. I'd rather err on the side of caution." She turned back to the Scotsman. "Carson, let us know as soon as we can speak to Dr Lepreux in the morning."

"Will do." He nodded and returned to his work. Elizabeth turned and began to walk back to her office and Caldwell fell into step beside her.

"If all these attacks are related, then they are acts of war."

"I'm all too aware of that, Colonel."

ooOoo

The door swung back with a screech; the light was brighter than he had expected and he screwed his eyes up as he looked at the two silhouetted figures in the doorway. One of them stepped forward into the cell; his companion shot a look of caution toward him but he ignored it, confident that he was in no danger. John had to admit that there was no way he could take on this guy in his current state, he was perhaps a little shorter than him but athletic in build, his light brown hair was cropped short. In this light, his eyes looked almost black and they betrayed no emotion besides a small amount of annoyance. Turning his head slightly to one side, he examined the damage Sheppard had done to himself during his assault on the door.

"Who are you?"

"You may call me Iestyn."

He looked at the uniforms the two men were wearing. "You're not Genii?" A curious look passed over the man who called himself Iestyn's face.

"No. Why would you think we were?"

"Let's just say they don't like me very much. So, who are you?"

"Our name would mean nothing to you if I told you."

Sheppard tried to remember what had happened. "We were with the Guennec…"

"We are not the Guennec, and I will answer no more of your questions." His tone was dismissive and irritable. "Do not worry, Colonel you shall not be left to such solitude again, your little tantrum is a timely one." As he took a step closer he wrinkled his nose in distaste "My men will take you to wash. That's for my benefit, not yours. If I am forced to spend time in your company, I'd rather you didn't smell like a dead rodent." The commander gave him one last disdainful look before walking away. When the guard, who had since been joined by another, entered the cell, John held out his hands defensively but ultimately in vain; he was in no fit state to fight. One of the guards grabbed his arm, twisting it around and forcing him face first into the wall. His hands were bound and he was hauled backwards toward the door, wincing at the light.

ooOoo

The tests on the bullets had proved conclusive; they were looking at the same people who had shot Granger. Suddenly a group of unfriendly natives had become something altogether more sinister. Three attacks on off world parties, one of them resulting in the loss of six lives. Even friendly worlds were no longer safe for them, not that there was anywhere that could truly be described as safe in the Pegasus Galaxy

Two of the teams off world had returned unharmed, a third was due to make contact in half an hour, the fourth an hour after that. Time seemed to be passing so slowly; sitting at her desk she used her pen to push the chain of her Grandfather's watch into patterns. She kept telling herself that the fact that they had heard nothing from either of them before the scheduled time was a good omen, that the old adage was right, no news was good news. Yet a hundred other scenarios had played through her mind. As Elizabeth sat alone in her office, she closed her eyes and was surprised to find herself offering up a silent prayer.

ooOoo

He woke up abruptly, gasping for breath, his muscles jerking with uncontrollable spasms; he was lying once again on the floor of his cell. They had taken him to a shower block, the high-pressure, icy water and caustic soap leaving his skin feeling raw. He'd examined the bruises on his body and watched as the water, coloured rust with blood and dirt, pooled in the gutter at his feet. Then they had returned him to his cell, still damp and shivering, newly shaved and his hair cropped close to his head. Looking around he could see the guard he had spoken to, Iestyn, standing over him, a weapon like the one the young boy had used to capture him hung in his hand. As his stomach tightened and he retched, Sheppard rolled over, gulping back air.

"It hurts, does it not? It has many different settings, it is a useful tool." His body continued to shudder. "You are lucky you have not eaten recently, prisoners have been known to choke upon their own vomit. It would be unfortunate if that should happen to you, we have much to talk about." Iestyn crossed the floor and peered down at him. "I have no real wish to hurt you more, though I will not hesitate to do so if you insist on being uncooperative. So, let us have an agreeable conversation, you and I. Tell me about Atlantis."

"Screw…you!" He had to force the words out.

"I do not know what that means, but I can guess." With a sigh the commander pulled the trigger again and another spasm of pain pierced through John's body; he screamed out until his throat felt like it would bleed. "Your intentions are honourable, but futile." Iestyn squatted down on the floor next to him, resting his hands on his knees, looking completely relaxed. He continued, speaking like a teacher to a child, "The longer you continue this stubbornness, the more you will suffer; if you will only help us then I can make your final days more comfortable. All you are doing is delaying the inevitable."

Struggling to control his own body, he didn't notice the priest enter the cell at first until Iestyn stood, his relaxed bearing immediately replaced by restrained hostility. "Patriarch Braen, I am surprised to see you here. I thought that I had been entrusted with this prisoner."

"I have little faith in your methods, Iestyn. So far they have proved fruitless."

"So have yours." The room fell silent, the only noise Sheppard's breathing and quiet whimpering as he fought for control of his own body.

"If you ever speak to me with such insolence again, you will gain first hand knowledge of just how effective my methods can be, Commander." The words were spoken quietly but with menace.

Twisting onto his side, he could see the newcomer watching him but he also noticed, behind him, Iestyn's jaw clench and his fingers twitch against the trigger of the weapon; there was clearly no love lost between these two. The Priest loomed over Sheppard and he got his first look at the man. The face matched the voice. He was stocky, his hair peppered grey and pudgy features sat in a ruddy face. As the man's booted foot connected with his stomach, John let out a cry and rolled over on to his back. The man kicked again, and he curled as tightly as he could into a ball, holding his hands over his head.

"What is your identification code?" It was the voice of someone who was used to being obeyed. Sheppard's body still twitched from the last hit from the weapon, each movement sending new pain through his body. Hands clasped hold of him, rolling him on to his back, pulling his arms away from their protective stance, and a second pair of hands, one of them scarred along the palm, pinned his shoulders to the floor while the priest placed a knee in his chest, restricting his already laboured breathing. Grabbing Sheppard's neck, the Patriarch" forced his head back and looked him in his eyes. "Tell us!"

"Won't do…you any…good." He coughed the words out and the weight on his chest increased as the man leaned in closer.

"TELL ME!"

"Been gone…too…long" And it was the truth; no way would Caldwell accept his IDC after all this time, protocol meant returning to the alpha site, where verification of who he was could be radioed through by the marines on duty there. Elizabeth would have opened the shield, she wouldn't risk killing him, wouldn't risk killing anyone, she wasn't built that way, but Caldwell was a military man through and through and would do the right thing, make the hard choices.

"He is telling the truth," Iestyn spoke up. "Consider it, in a similar situation we would do the same. They will not lower the shield for him, we will have to work on one of the others." _Others? _There were others? His heart beat even faster in his chest until it felt as though it would explode and blood rushed to his head. The man looked down at him in disgust before slamming Sheppard's head back into the cold stone floor. He felt a warm rush of blood in his hair. "It would be better to just kill him now, he is of no use to us." Iestyn reasoned.

"No. You know that there is an agreement, our friends would not be pleased if we let him die too soon." The pain in his head was searing, and his vision blurred, dark shapes floating in front of his eyes, slowly he closed them and let relief wash over him as once again he drifted into nothingness.


	8. Masks

_A/N - As always, many thanks to those of you who took time out to review. Remember this is my first fic so feedback is really helpful. Now I'm rather worried about your reactions to the ending of this chapter I hope you're not too disappointed in me...  
_

* * *

**Chapter 7**

**Masks**

How long he'd been unconscious he couldn't tell. Moving really wasn't an option, his limbs wouldn't respond the way he wanted them to and he'd discovered a whole new kind of exhaustion. So he simply lay there, concentrating on each painful breath. A boot nudged him in the ribs, making him moan, and he felt hands around his wrists; he was dragged across the floor and rolled onto his mattress. Feeling a hand against the clammy skin of his forehead, he winced away from the touch. He opened his eyes and, through blurred vision, he could see Iestyn crouched. He opened his eyes and was met with a blurred vision of Iestyn crouched down beside him, assessing his injuries with an impatient expression.

"If he wants to keep you alive he really should not have tried to break your head open on the floor," the guard sighed in annoyance.

"You the good cop?" Iestyn cast him a puzzled glance. "Bad cop, good cop; one scares you, the other befriends you, tricks you into talking." John explained. "You're definitely the good cop."

"Good? I just tortured you." Iestyn dipped a cloth into a bucket that reeked of disinfectant and held it over the wound on the back of Sheppard's head.

"I'm not taking it personally." He drew in a sharp breath as the cloth was pressed into the wound, a hot stab of pain shooting through his head, and he felt the cold liquid run down his neck. As the cloth was replaced in the bucket John gestured to it. "Why?"

"I don't want you dying of an infected wound before we break you."

"That's…nice."

"Well, I am the good cop." Amusement flickered in the commander's eyes as he got up to leave.

"Wait. Why did he call me a heretic?"

"You do not know?" Iestyn sounded incredulous.

"No."

"Because you occupy the Sacred City and dishonour the memories of the Ancestors."

Sheppard groaned. He had little time for organised religion; he'd seen first hand the atrocities carried out in the name of God. They'd met people in the Pegasus Galaxy before who had worshipped the Ancients, but they had always been peaceful and they'd never before met any fanatical enough to attempt to do this.

"And what you're doing doesn't dishonour them?"

"We have right on our side."

"That's what they always say." Gently, and with a great deal of effort, he rolled himself over to relieve the pressure on his most painful injuries. "We're not occupying it, Atlantis is our home."

"Not for much longer." John felt his blood run cold at the certainty in Iestyn's voice. "You don't have long to rest, make the most of it."

ooOoo

Lieutenant Jacob's team had returned without incident. Elizabeth watched from the control room balcony as Colonel Caldwell apprised them of the situation, their military stoicism masking their shock and grief; she knew how they felt, she wore a similar mask herself. Lorne's team had been due to make contact an hour later, that deadline had passed 40 minutes ago.

Since Colonel Sheppard's disappearance, she had come to rely on Lorne a great deal. Although Caldwell had become familiar with the way things were done on Atlantis and was up to date on all the reports and procedures, unlike the Major, he hadn't been out in the field and he didn't know every serviceman and woman by name. Lorne did. His experience and natural affability made him indispensable when it came down to the everyday running of the city and she had hoped his presence would ease the change of command.

There were more people in the control room than necessary but much of the senior staff, both military and civilian, had found an excuse to be there. Carson had arranged for a med team to be standing by as soon as he learned that the team was late checking in. Rodney was busying himself at a console, searching through the database trying to find any connections between the planets where the ambushes had taken place, so far without much luck. Frischmann sat beside him, asking occasional questions, and remarkably McKay had only snapped at her a couple of times.

ooOoo

This time, when they came for him, one of the guards carried a syringe in his hand. Panic swelled in his gut and John dropped to the floor and crawled into the corner, trying to escape the needle. When they came toward him, he kicked out, but he was grabbed by the ankles and dragged out flat on the floor, screaming, kicking and punching. His old injuries exploded in pain but he still fought. Two guards held down his thrashing legs while Iestyn put a knee in his chest and held his shoulders flat to the hard stone floor; he felt his arm pulled out straight and the barely detectable sting of the needle. Looking up in to the eyes of the commander he thought he saw a hint of regret.

His mind was so fogged he could barely hold together a coherent thought; he sat huddled in the corner of the cell, his body jerking uncontrollably. They'd bound his hands in front of him and the bonds cut deeper into his wrist with each involuntary jolt of his muscles.

Iestyn sat facing him, patient and relaxed. "What is the population of Atlantis?" The commander reached into his pocket and pulled out Sheppard's tattered wristband; he toyed with it in his fingers before stretching it over his own wrist. Sheppard watched the piece of black fabric, wanting to rip the man's arm off to get to it. "What is the ratio of military to civilian, what harm can it do to tell me that?"

"Six to one."

"See, that was not so difficult was it? Such a shame that it was a lie. If you had told me the truth I would have let you have this back." Iestyn pulled the sweatband off his wrist and held it up. "It means a lot to you doesn't it? What does it signify?" Sheppard said nothing; it held no significance to anyone but him. "If you tell us how to infiltrate the city with minimum casualties, we will let the civilians go free." Iestyn had a habit of changing the direction of his questioning suddenly, John knew this was a tactic designed to confuse him and all the while the commander spoke in his calm, soothing voice.

"You already killed Weir and McKay." Something flickered across the commander's eyes, something he couldn't read.

"That was necessary, they were not ordinary civilians. Was she not the leader of your people, the one who sanctioned your actions?"

"Actions?"

"You awoke the Wraith."

"Accident." He mentally winced at the word but it was true; he had accidentally awakened a race of life-sucking aliens that terrorised an entire galaxy. It was the sort of thing that could only happen to him.

"An accident?" Iestyn smiled him. "Tens of thousands of lives lost - that is a most unfortunate accident. Why do you keep the city from its rightful heirs? Hmm? The Ancestors left Atlantis behind to protect their children and yet here you are, from another galaxy, stealing our birthright." Tens of thousands; the words echoed in his head, the image of Sumner kneeling before the keeper, the life draining from him, the bullet piercing through her hand and into Sumner's heart.

"They…they came from our world."

"Who?"

"Ancients…Ancestors." Iestyn stood shaking his head, anger flashing through him for the first time.

"Your heresy knows no bounds, does it?" He sighed, gesturing to the other guards. "Maybe we can persuade you to be honest with me." Once again, he found himself dragged out into the middle of the floor and pinned down. "Perhaps Braen's methods have some merit after all." Iestyn crouched down, taking hold of his hand, and Sheppard screamed at the sickening snap as his first finger was broken.

ooOoo

When the gate finally activated an hour an thirty-three minutes after the scheduled time, the tension in the control room was unbearable. Elizabeth stomach was in knots and she felt both hope and dread in equal measure. The room was utterly silent as they waited for an IDC. When the gate technician finally spoke, he had the undivided attention of everyone in the room.

"Receiving Major Lorne's IDC." There was a collective sigh as everyone released the breath they were holding, but the tension in the atmosphere didn't dissipate just yet.

"Lower the shield." She watched, her heart still in her mouth. There was no radio contact, which was a good sign, but still it seemed an age before the first members of the team came through the gate. They looked around them with puzzled expressions at the relieved faces that greeted them from the crowded control room as they each stepped through the gate unharmed. Elizabeth ran down the stairs to join them, striding out toward the gate as the wormhole shut down behind them.

"You're late, Major." Her tone was a mixture of annoyance and relief and Lorne gave her a sheepish grin; he knew how much she hated teams checking in late, it just gave her even more things to worry about.

"Yeah, sorry about that ma'am, but we ran into an old friend."

ooOoo

_His footsteps echoed through the empty city. The lights came on for him but as soon as he had passed by, they died. In the control room a thick coat of dust covered every surface. The air was stale and dry. Turning toward the balcony, he saw that the doors were wide open and the dust was blowing in through them; he stepped outside but, where there should have been ocean, grey desert stretched out toward mountains. He turned back to the city but it had disappeared and he found himself back at Khandahar._

_Noise flooded in around him, Black Hawks passing overhead so close he felt he could reach out and touch them. He watched as a med evac touched down on the tarmac; the medics rushed forward, dragging stretchers along behind them. He walked slowly over toward them as they busied themselves around the helicopter. A body was pulled out, bloodied to the point of being unrecognisable, its arm only hanging on by a few tendons, the flesh torn away, deep crimson soaking through the uniform; an Atlantis uniform. He watched as more bodies were pulled from the chopper, each one with horrendous injuries, each one in the same grey uniform. He looked across to the lone pilot and met his own eyes looking back. _

He awoke with a shudder. Rolling over, he vomited, bring up the small amount of bread and water he had been given to eat. Turning back to lay on his mattress, he tried to remember what had happened; his left hand screamed in pain and he laid it gently on his chest, trying not to move it any more than necessary. Iestyn had talked and talked, barraged him with question after question, the drug mixed with the pain had fogged his brain so much he couldn't remember what he had said. Had he answered? He couldn't be sure, he could only remember the relief when he finally felt consciousness drifting away.

"What is the gene?" The voice in the dark startled him. He had assumed he was alone in the cell but now, looking around, he saw the shadowy figure of Iestyn sitting against the wall next to the door.

"What?"

"You spoke of a gene. What is it? What does that mean?" No matter how hard, he tried the memories wouldn't come to him. Panic rose in him when he realised he couldn't remember what he had told them.

"I don't know." A deep impatient sigh came from the other man.

"When will you learn? Do you really wish to return to your solitude? It can be arranged. I know that being alone was more of a torture to you than this; the pain gives you something to fight. I understand that. You see we are not so very different, you and I."

"I'm nothing like you."

"If that is what you wish to believe, go ahead but you are wrong." Iestyn sat in silence for a moment and Sheppard could hear the man's steady breathing. When he spoke again his voice was quieter, little more than a whisper in the dark cell. "I confess I am confused; so many things I have been told contradict themselves. We are taught to follow the orders of the council without question yet I find my head swarming with them. The Patriarchs tell us that this is the right path for us, that the prophesies have come to pass and the Ancestors are being reborn. I have seen with my own eyes that they have revived the relics in the temple…yet still I do not trust them." He paused thoughtfully. "And then there is you. You, Colonel Sheppard, are the biggest contradiction of all. I do not understand why we are keeping you alive, we will gain no strategic information from you, of that I am certain. No, there is something more, something I am not being told."

"Reborn?" Of everything that he had said, that was the one phrase that stood out. _The Ancestors reborn_.

"Yes, but you know that, you needed their blood to bring the city to life." Iestyn said dismissively. John wondered if any of this would make more sense if he had been able to think with a clear head and came to the conclusion it probably wouldn't. Fighting against the fog in his mind, he tried to explain. If there was even a small chance that he could convince this man he was wrong, he had to take it, though the words came slowly.

"No…I don't understand…no blood…just us."

"Us? The technology of the Ancestors can only be activated by one who carries their blood in their veins, so you must have needed them; it is claimed that you personally killed over sixty of their people."

"No… no…we never…" Past mistakes had often came back to haunt him, but this one wouldn't be put to rest. He knew now why Iestyn hadn't been allowed to kill him, because you couldn't take revenge on a dead man. It all began to fall into place and he felt a mixture of anger and fear boiling inside him. "You're…you're talking about the Genii."


	9. Issues Of Trust

_A/N - Well here it is chapter 8, sorry about the delay. Thank you once again to all of you who took the time and trouble to review the last chapter. now personally I'm not so keen on this chapter but what do I know? _

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**Chapter 8**

**Issues of Trust**

Iestyn stood up and Sheppard could sense the tension in the man's body even from across the room. "So it is true then?"

"They tried to take the city…I had no choice."

"You were holding their people hostage." Anger had crept into Iestyn's voice.

"No." With considerable effort, he pushed himself into a sitting position and stared through the dim light, searching out the other man's face. "No. They tried to take the city by force, I had no choice." Each sentence seemed to leave him out of breath. "I was protecting my people. You'd have done the same." Iestyn had stopped pacing and was watching his face closely. He could only try and explain, trusting this man was a risk but one he had to take. "The ATA gene is…" He patted his chest lightly, the proper words not coming to him. He searched for a simple way to explain it. "The part…the part that comes from the Ancients. When they left Atlantis they returned to my planet…and…um…I guess they interbred with my people...their descendants carry the gene."

"I have seen the Genii activate the relics in the temple."

"Gene therapy. Transplanting the gene into someone born without it."

"That is possible?" Iestyn sounded incredulous.

"Yes. They…they took samples. Some of my men, they took them hostage." His head was still cloudy; confusion was fast becoming his natural state of mind. He growled in frustration. "I can't explain it properly… I'm telling you the truth. Only wish I could prove it."

Iestyn breathed out, clearly agitated, and abruptly he moved toward the door. "I will return shortly."

ooOoo

The puddle jumper sat waiting in front of the gate. Elizabeth settled herself inside beside Ronon while Teyla sat up front next to Frischmann who nervously tapped her foot on the floor as she went through her pre-flight checks. Although she had been spending every spare moment in practise flight around the planet, this would be the first time she had taken a jumper off-world. Elizabeth looked up at the control room through the still-open hatch and Caldwell frowned back at her. He wasn't happy about this and she couldn't blame him, she was more than a little nervous herself. The technician began the dialling sequence.

"Hey! Wait for me." Rodney hurried across to them, still adjusting his vest. Standing and hitting the button to stop the back of the jumper from closing, Elizabeth raised an eyebrow at Rodney in annoyance.

"Rodney, what are you doing here?" He looked up at her, his face determined.

"This is my team, I'm going."

"I don't think so. You're supposed to be taking it easy, remember? Besides this could be a trap."

"Well, duh! And if it is a trap you may just need a genius to get you out of it." She was familiar with the expression on his face and knew that he was determined and the fact that he actively wanted to come along was a positive sign that he was beginning to accept life without John. Not wanting to knock his confidence, something she had once thought impossible, she relented.

"Very well. But just…keep your mouth shut." He was about to protest but she interrupted him. "This is our chance to find out what the hell is going on, I don't want you sticking your foot in it. Face it Rodney, diplomacy is not your strong point." He seemed to consider this for a moment and then shrugged, conceding the point. As the wormhole whooshed out into the room and Rodney took a seat at the back of the jumper, Caldwell called down to them.

"Be careful, Doctor."

"Don't worry Colonel, I intend to be."

"Captain, the first sign of trouble and you get her the hell out of there."

"Yes, sir."

"Good luck." Elizabeth smiled and nodded at the Colonel as the jumper door closed; he frowned back disapprovingly. He was right, it was foolish of her to be going off world at a time when they were all in danger, and to be going with limited weapons and security was just plain stupid. Nevertheless, it had been her decision and if he was going to be the new military commander of Atlantis, he'd have to get used to her stubbornness.

They flew out the other side of the gate into twilight; the town sat maybe two miles away, reminiscent of a hundred other settlements they had come across since their arrival in the Pegasus Galaxy. Parking the jumper a few hundred yards from the village, they cloaked it, walking the rest of the way. Small stone houses were huddled together on narrow streets. As they walked past they saw that many of them stood abandoned, silent memorials to those taken by the Wraith. The streets were mainly empty, just a few farmers returning from their fields, in the houses lamps were being lit and wisps of smoke rose from the chimneys as the evening turned cooler.

The large tavern was at the centre of the settlement, set back in a small courtyard. It was the focal point of the town and, as such, was crowded with locals unwinding after a hard day's work. The sound of laughter rang through the windows and the tantalising smell of cooking wafted out through the door. As they entered, faces turned to them and they were welcomed with warm smiles and raised glasses. They were used to visitors from other worlds here and the people were acquainted with the Atlanteans, having traded with them on a regular basis. It was why Elizabeth had agreed to meet here. She returned their greetings politely, scanning the packed room. Teyla leaned toward her.

"She is not here."

"Anyone else you recognise?"

"No."

"Then I guess we wait."

ooOoo

Iestyn came into the cell with an uncharacteristic nervousness.

"We must be quick." Sheppard found a small black cloth bag placed on the ground in front of him. "If it is found missing, I…" As he unfolded the bag, revealing it's contents, his words faded away. "You wanted a chance to prove to me you were telling the truth."

He held the item up; it was a small pyramid-shaped artefact of typical Ancient design and, taking John's good hand, he gently placed the device in his palm. As soon as it touched his skin, it began to emit a soft light, then a small star map appeared, projected above it. Through the hologram he saw the tiny stars and nebulas reflected in Iestyn's dark eyes and a childlike wonder lit up the commanders face.

"I knew it." Iestyn's voice as quiet as a breath.

They watched the tiny spinning galaxy and John found himself lost in the device, reaching deep inside it. His mind, seeing a chance to escape from this cell, pushed further until it felt like he was floating out among the stars. As he drifted, his thoughts turned to home and the hologram shifted and then it was as if he were flying through the stars, ever faster until they became just a blur. Eventually, he entered a solar system and everything slowed down as he was drawn in to a large planet; gliding down through the atmosphere and above a wide blue ocean, he arrived home. Cupped in the palm of his hand, he held a tiny version of his home, it's many spires recreated in miniature. Tears of longing escaped his eyes. For so long he'd been unable to conjure up the image of her in his mind; the harder he had tried, the more the idea of Atlantis had slipped away from him. The only place he could see his home was in his dreams and then it was a twisted, hostile version.

Iestyn gasped, his voice filled with reverence. "It is beautiful."

"Yes, it is." But the guard's voice had broken the spell and he realised with horror what he was doing; he shut the image down, his heart breaking as Atlantis faded away. If this artefact held an image of Atlantis, what other kind of information did it hold on the city? How could he have been so stupid? Gathering his strength, he hurled the object across the room, slamming it against the wall. It rebounded and landed near Iestyn's feet and he picked it up a look of shock on his face.

"What is wrong?"

"Get out." John hissed, his anger directed at himself as much as the man in front of him.

"You must understand. I have witnessed the Genii activating the relics, I have seen how they must concentrate and even then they struggle to control it. But you…" Iestyn exhaled heavily, dropping his head as understanding dawned. "…you do not trust me. I would not trust me either in your shoes."

"I don't have any shoes, you took them away." The vulnerability of being barefoot had never really occurred to him before, he'd always associated it with a feeling of freedom, the sand between his toes. But now it made him feel fragile.

Returning the artefact to the bag and folding the cloth around it, the commander stood up. "I wish I could stop this madness, for all our sakes."

"Then let me go. I can end this."

"You know I cannot do that."

"Then kill me and get it over with!"

"I cannot do that either." John turned away, unable to look at the pity in Iestyn's eyes. "I am truly sorry." Something soft was pressed in to his right hand; he lay there until the footsteps had echoed away and then awkwardly, using his teeth, he pulled the threadbare sweatband over his wrist.

ooOoo

Elizabeth had thought to bring a small amount of spices to trade and the landlord was happy to provide drinks in exchange. They found a table in a quiet corner with a good view of the rest of the room and easy access to the door. As they sat quietly, nursing their drinks, the locals carried on their rowdy conversations around them.

All of a sudden, angry voices rose above noise; accusations flew and shoves turned into a scuffle. A punch was thrown and the victim staggered backward, tumbling into their table, barrelling into Elizabeth and knocking her from her chair. Ronon grabbed the man by his collar and hauled him up, dragging him back across the room to his attackers and dropping the unfortunate man in front of them.

"Apologise to the lady." Ronon never raised his voice; he didn't have to.

Elizabeth called across as Teyla helped her to her feet and she brushed herself down. "Ronon, I'm fine, it was an accident." Ronon turned to look back at her and, as he did so, one of the men swung his arm out and Elizabeth felt her breath catch in her throat as she caught the gleam of a blade in the drunkard's hand. Ronon moved fast, the blow was stopped in mid-air as Ronon grabbed the assailant's wrist; swiftly he twisted, forcing the man to drop the knife, and with another sharp movement the man was on the floor. There was a moment's silence, like a deep breath before the plunge, and then all hell broke loose.

It seemed like the whole tavern had erupted into one massive brawl and at the centre of it was Ronon. Elizabeth looked at the scene in despair; she could negotiate peace treaties between rival nations and despotic leaders but didn't have the slightest clue of how to calm a drunken brawl. Teyla turned to Frischmann and McKay.

"Get Dr Weir back to the gate. I'll get Ronon." And, with that, she too disappeared into the throng.

"Damn it!" The captain set her jaw, her eyes burning with anger as they followed the Athosian. "Did they behave like this with Sheppard?"

Rodney shrugged. "Pretty much."

"Great!" Putting herself between the mob and her charges, she began inching them toward the door, her hand resting on her side arm. The room heaved with people, the shouting raised to the deafening level of a full-scale riot. Once outside, the three of them stepped up their pace, heading back through the almost deserted streets of the village, Frischmann eager to get them back to the safety of the jumper.

Rodney was soon panting with the exertion as Frischmann pushed them onward, her sidearm now drawn; as part of the deal the P90s had been left behind in Atlantis. They had reached the outskirts of the town when suddenly a movement in the shadows caught Elizabeth's eye; she barely had time to cry out as a stunner blast hit Frischmann, she could only watch as the captain fell to the ground mid-run. She knew turning back was a mistake, that it would only mean they would be captured, but she couldn't abandon the Captain. Skidding in the dusty street as she turned, she hurried back, Rodney at her side. Grabbing hold of an arm each, they tried to raise Frischmann to her feet. Elizabeth stopped dead when she felt the unmistakable pressure of a gun barrel against the base of her skull. Casting a sideways glance at Rodney, she could see his wide-eyed expression as he too froze.

"Leave her!" Lowering the Captain gently to the ground, they slowly turned, their arms roughly grabbed, and they were ushered out of the main street. They found themselves being quickly hustled down the streets of the village, past locked doors and shuttered windows. They were pushed harder, each of them with an arm in the grasp of one of their attackers. Although they were being kept off the main street, Elizabeth soon realised where they were heading - back to the jumper. Sure enough, as they left the outskirts of the town she could see a small group standing around the place where they had left the small space ship, invisible beneath its cloak. Their arrival had been observed.

As they neared the spot where they had left the jumper, legs aching and chests burning at the pace they'd been forced to maintain, one of the group stepped out to greet them. The woman they had come to meet - Sora of the Genii.


	10. Powerless

_A/N - A nice quick update this time. And as always thank you very much to those of you who took the time to leave feedback. Just a quick warning for violent imagery in this chapter. I hope you enjoy.  
_

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**Chapter 9**

**Powerless **

Sora had changed little since Elizabeth had last seen her. She had stayed on Atlantis until the truce with the Genii after the Wraith attack on the city and they had heard nothing from her since. Now they stood here in the dark, beside the cloaked jumper. Elizabeth glared her.

"We came here in good faith. I thought that our two peoples had finally put our differences behind us.

Sora didn't answer, she merely paced agitatedly. "Where is Colonel Sheppard?"

"What?" Elizabeth furrowed her brow in confusion. "What does the Colonel have to do with anything?"

"I had assumed you would be bringing him with you." Sora gritted her teeth and looked at Rodney. "Well, you'll have to do."

Rodney's voice raised a pitch in panic. "Do for what?"

"We need a jumper pilot."

"But…but I can't even fly in a straight line."

The Genii woman sneered at him. "Like I said, we were hoping for Colonel Sheppard."

One of the men grabbed Rodney's arm roughly and dragged him toward the ship. "Open it." He looked toward Elizabeth; as he did so Elizabeth felt a gun pushed against the back of her head and she could see the sudden bolt of fear in Rodney's eyes, not for himself but for her. Reluctantly, he did as he was told. Once the hatch had descended, he was pushed inside.

Sora walked closer to Elizabeth. "I have no argument with Atlantis and Doctor McKay will come to no harm by my hand. Now be quiet and listen, there's little time. The Genii are pulling themselves apart. Ladon's leadership has been found wanting and the people are looking for guidance elsewhere. Kolya has…"

"Wait, Kolya? We were told he was dead."

"Not dead, just in hiding. After the coup he began to gather people to his cause. There is a race called the Irith, they were part of the old alliance of worlds. But for centuries they have isolated themselves from the rest of the galaxy, few know of their existence at all. They are a devoutly religious people, worshipping the Ancients like gods. Kolya has filled their minds with lies and propaganda; he wants Atlantis, and now he has an army to help him."

"They're the ones who've been attacking our teams?"

"Yes. And right now they are holding two of your men hostage; part of our plan is to get them back for you." Three bodies hadn't been recovered from the attack on Ripley's team.

"Do you know who?"

"A soldier and a scientist. I'm sorry but that is all I know."

"Why are you doing this?"

"If there is one thing I learned from my time with you, it's that we need to stop fighting each other and work together to defeat the Wraith. I am tired of watching my people die senselessly. Our intention is to infiltrate the Irithian city; we have evidence that Kolya is plotting against them. We will secure the release of your men and send them and Doctor McKay back through the gate."

"With the jumper?" Elizabeth already knew the answer to her question.

Sora held her gaze. "Our scientists believe our own gene therapy is close to completion. What is one little space ship compared to all the wonders of Atlantis? Goodbye, Doctor Weir, and good luck." Sora turned and climbed into the back of the jumper, followed by three more of her men. The door closed and Elizabeth could do nothing but watch as the ship took off and headed toward the gate. Two men remained guarding her until the jumper was out of sight and then they too disappeared into the dark.

Elizabeth's lungs burnt as she ran back toward the town; she cursed her lack of fitness and swore she would put in some gym hours when she had the chance. She stumbled in the dark but, as she sped through the outskirts of the town, she could see three familiar figures in the faint light emanating from the houses, Ronon's unmistakable silhouette in the lead. She called out and he came running forward to meet her.

"Are you alright? Where's McKay?"

"I'm fine…but they've taken Rodney," she panted.

"Sora?"

"Yeah. We've got to get back to Atlantis but they've taken the jumper." She saw the muscles in Ronon's jaw working; a sound almost like a growl escaped him.

"I'm sorry, Doctor Weir. This is my fault. I shouldn't have abandoned you."

"You were set up, Ronon, but we can talk about that later; we have to get back to Atlantis as soon as we can." The thought of the long walk wasn't a pleasant one but she had no choice. Ronon offered an arm for support and she took it gladly and, with Teyla holding up a still weak Frischmann, they began their slow journey back to the gate.

ooOoo

This time he didn't resist when they came for him. He didn't want to risk further injury to his already broken fingers and fighting was futile anyway; he would just have to take what ever they dished out and hope he could shut out the pain. The whole of his hand was swollen and had turned an alarming shade of purple. As they bound his wrists behind his back, the pain made him retch but there was no food left in his stomach to bring up so he just choked back the acid rising in his throat. Iestyn wasn't with the guards, instead he found himself at the mercy of the priest Braen. Did that mean Iestyn had been discovered returning the device to the temple? Or was that all a ruse after all? More than anything he wanted to believe in the man, in what he had said. He knew he would never go home, that whatever course they were on he was powerless to stop it, but he felt an overwhelming need to have someone on his side, even if it couldn't change anything.

The drug felt different this time as it slid through his veins; it felt heavier, weighing his body down, making his tongue feel swollen. Braen watched him a satisfied look on his face as he sunk further into the depths of the drug; his mind slowing down, clouding until he felt like he was floating far away.

"Seeing as you will not tell us what we want to know, we must resort to other means; it is only fair that you should bear witness." Taking hold of Sheppard's jaw in his hand, his finger nails digging into the sides of his face, the priest looked him dead in the eye. "Soon each and every one of your people will be hunted down and executed and we shall see a new era in our galaxy."

Through swimming vision, he watched Braen's face. This was a man who thrived on power; torture and murder were just an added bonus, another way that he could play God. This man would have no problem in sacrificing the lives of others for his own ends. Sheppard thought of Caldwell; did he know what he was facing? Elizabeth would not have been equipped to deal with this, he could only hope that Caldwell would be able to make the difficult decisions that he would face in the days to come.

Thinking back, he remembered the sound of the Genii strike force thudding against the shield. He'd only spoken of it in his report to Elizabeth and during the debriefing back on Earth, relating the events of the attempted invasion in cold military terms. He'd never told anyone but he was still haunted by those dull thuds, each one a life, a soldier just following orders.

Slowly his eyes closed. Part of him wanted to fight for consciousness but the nothingness of sleep was tempting, he let himself fall into it, wrapped in darkness, only to be awakened by a sharp pain across his face. Snapping his eyes open, he saw Braen standing in front of him, his nostrils slightly flared in anger. He backhanded Sheppard around the face once more.

"You will want to stay awake for this." Turning, he walked out of the room. "Bring him!"

They pulled him from the cell and, one either side of him, hauled him down the corridor, his legs dragging along the floor behind him. It was as though his muscles had turned to water, he barely had the strength to lift his head. The room he was taken to was as bare as his cell but considerably bigger and brighter. He was forced to his knees. His head lolled back and he felt himself begin to fall to one side; a boot to his ribs felt more like a knife blade and he straightened up, willing himself to stay upright. Forcing his head up, he stared through blurred, floating vision as two other prisoners knelt in front of him. The effort it took him to concentrate on them left him exhausted. As he struggled to bring the two figures into focus he realised through the stupefying effect of the drug that they were familiar to him. He furrowed his brow, trying to make the connection; the name McCormack came to him and he felt his heart sink. They had said there were others.

It was as if the marine took a moment to register who he was; he guessed he looked a very different man to the one who had left Atlantis - how long ago? It felt like a lifetime. Shock flashed in McCormack's eyes but he recovered himself quickly.

"It's good to see you, Sir." One of the guards, the one with the scarred hand, booted the marine in the side.

"You were not given permission to speak."

Sheppard took in the room as best he could. Iestyn was still absent and that worried him. Braen stood watching the proceedings from the back wall, his expression almost one of delight; whatever was going to happen here, he was looking forward to it, the anticipation practically radiated off him. The other prisoner, the one who John's uncooperative brain couldn't find a name for, whimpered in distress; he was breathing deeply, trying not to give in to the shuddering sobs that overcame him every few seconds. John wanted to say something, to try to comfort them, but his throat was numb and his tongue felt swollen in his mouth. A hand touched the top of his head and tipped it back and he found himself looking up into a smiling face, another face he recognized. His mind provided a name for this one without hesitation; Kolya.

"Colonel, you really don't look like your old self. I almost feel sad seeing you look so pathetic, so weak and defenceless. Broken." Kolya savoured each word; he smiled at the Patriarch before turning his attention to the other two prisoners. "Now, which one of you is going to tell us what we want to know?"

McCormack was the one to speak. "Not going to happen."

"Are you sure about that?" The sergeant held his gaze defiantly.

"I had a feeling you would say that." Kolya nodded and Sheppard saw the Patriarch's fingers go to his ears as the gun was pulled from its holster. The report echoed in the small room making his head ring. Warm blood hit his face as the bullet impacted against the sergeant's head and McCormack's body slumped to the floor, a gaping hole in his skull. The nameless scientist threw up, the pool of vomit mixing with the blood on the floor. When the guard placed the pistol against the scientist's head, his retching and sobbing became almost unbearable to listen to.

"Please. Please." He begged them, his voice thick with tears, as Kolya crouched down beside him.

"I'm not enjoying this but I will do whatever is necessary. You've seen that. " He took the man's head in his hands and forced him to look at the corpse of the soldier, before moving him to focus on Sheppard. "He's been here for months, months of torture and pain. Look at him, just a shadow of his former self, his mind as broken as his body. Is this really how you want to spend the rest of your pitiful life?"

"No." His sobs quietened, his voice little more than a whisper. "I'll…I'll tell you."

"No." Sheppard surprised himself by speaking. "No." The word was heavily slurred, but he could see the doctor understood. The scientist looked torn; he didn't want to betray anyone, but he didn't want to die either. Sheppard tried to hold his gaze, tried to give him strength through the connection, but Kolya moved quickly, standing up and taking one of the guard's rifles, bringing the butt of it down on Sheppard's head. A hot needle of pain shot through his head but he clung on for a few seconds more, holding eye contact with the scientist. "No."


	11. Geniuses Rush In

_A/N - Here we are again. To those of you who have been kind enough to leave reviews my thanks. I hope you enjoy this chapter. _

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**Chapter 10**

**Geniuses Rush In**

Rodney felt utterly miserable; the Genii uniform he now wore was scratchy and clearly designed for someone both taller and thinner than himself. The fabric pulled tight across his chest, restricting his breathing and making him feel claustrophobic. Sora and her little gang of rebels busied themselves in preparation around him, their expressions earnest. Much to Rodney's dismay, he'd discovered that only himself, Sora and one other Genii, a tall youth called Peran, would be going; they would rendezvous with a man they had on the inside once through the gate.

He settled himself into the pilot's seat, taking in deep breaths to calm himself. They hadn't been impressed with his piloting skills on the way here but what had they expected? Flying a jumper at the best of times required concentration but, when terrified, it took on a whole new level of complexity. The plan was to fly through the gate quickly and cloak as soon as they were out the other side; then it was a case of parking up somewhere discreet and slipping into the city. Of course the jumper would be spotted by the guards at the gate but they would be looking for Atlanteans not four Genii soldiers. That was the plan. Rodney thought the plan sucked.

Concentrating hard, he took off, manoeuvring the ship around and heading for the gate. He could feel the anxiety radiating off of his companions, something that only served to amplify his own apprehension. Sora sat beside him quietly, looking ahead. As the gate came into view she dialed the address. The event horizon shimmered into existence and they sailed through it into dawn light. Guards were stationed around the stargate and, before he could engage the cloak, they started firing off shots at the jumper. Once invisible, he made a sharp turn to the left, leaving the trajectory they had been observed following, trying to remember all the things Sheppard had taught him.

The planet was mountainous and the gate sat in the foothills of a snow topped mountain range. Sora pointed out a spot to land cradled inbetween rocks and trees. It was an awkward manoeuvre and he received some dirty looks from the two Genii as the ship rocked back and forth but, after a couple of abortive attempts, he managed to set the jumper down in one piece. There was a collective sigh of relief.

"Do you have a life signs scanner, Doctor?"

He pointed to a rucksack at the back of the jumper. "In there." Peran chucked the bag at him and he caught it clumsily. "Any life signs close by?"

He pulled out the handheld device and activated it. "In the woods, about a hundred yards away. One single lifeform big enough to be human."

Sora seemed to relax slightly. "That should be Narim. Come on."

They left the safe confines of the jumper and headed into the woods, Rodney looking back wistfully at the spot where the concealed ship sat. They had only been walking for a few moments when a dark, stocky Genii appeared in front of them. He greeted Sora and Peran with a relieved smile.

"We should move quickly. Your arrival has heightened security; they have called reinforcements in to guard the entrance but that could work to our advantage, with any luck we should be able to just walk into the city unquestioned."

"With any luck?" Rodney hissed as he threw his hands up in the air. "Fantastic! This plan just gets suckier by the minute." Sora grimaced at him and nodded to her men to keep moving. Another ten minutes walking took them within sight of a group of Irithian soldiers who gripped their weapons tightly, the crackle of radios serving to reinforce the tension in the air. They guarded what appeared to be a temple. At first glance the structure appeared to be Ancient but, as they drew closer, Rodney realised it was nothing but a crude copy of the Ancient architecture, embellished with statues of figures in epic poses on either side of the entrance.

True to his word, Narim lead them straight toward the soldiers at the temple; all McKay could do was follow. A couple of the Irithians turned sharply at their approach, drawing the attention of another guard who bore the unmistakable air of an officer; he stepped forward and greeted them.

"Narim, what were you doing in the woods?"

"We circled round from the gate looking for the Atlanteans, Sir. We found nothing. Have there been any further sightings?"

"No." The Irithian officer glanced nervously at the sky before returning his gaze to them, regarding Rodney, Sora and Peran. After a brief moment, during which the scientist held his breath, the officer seemed to lose interest. "Are you heading back to the gate?"

"No Sir, we have orders to join General Kolya inside." Once again the officer paused for a second before nodding to the guards at the entrance of the temple. The guards parted and their small group traipsed past into the temple. Inside more statues lined the walls, Greek style gods and heroes. At the back was an Altar and behind it a screen was pulled back revealing a most unlikely addition to the classical temple; a huge, rusted metal door. As they approached Narim pulled out a piece of paper and handed it over to one of the guards who inspected it and handed it back. The massive door was pulled back and they stepped inside. They passed through a second guard room on the inside; once out the other side Rodney stepped up beside Sora.

"Kolya?" Rodney hissed through gritted teeth. "Kolya's here?"

"Of course he is."

"But he'll recognise me."

"We have no intention of letting him see you."

"Well that's not very…" But Rodney's words dissolved in his mouth as he got his first proper look at the Irithian city.

Rodney was impressed. And it took a lot to impress a genius. The city was vast. They walked along a wide balcony overhanging a vast natural chasm; unlike the dank tunnels of the Genii, here were wide, well lit walkways. Looking over the balcony made him woozy with vertigo, but he found himself unable to look away, awestruck by the sheer scale of the city. On the other side of the chasm he could see what appeared to be a residential area, homes cut into the mountain, painted courtyards standing in for gardens; he could see a group of children playing with a ball. What he had expected was something akin to the Genii complex; dark, uninviting and basic. He hadn't expected this living, vibrant city.

If the Irithians and Genii had been allies centuries, millennia in the past then maybe the tales of this city, this engineering work of art, had been the basis for the underground world of the Genii. But the Genii complex was a shadow of this place. The more he looked, the more he felt as though he was looking at something out of fiction.

The four of them walked in silence through the city, Rodney having to stop himself from staring. This side of the city seemed to be almost entirely populated by military and again they were a little more alert than the average soldier on guard duty. No one was getting in or out of this city without permission, which wasn't a comforting thought.

"So what now?" he asked Sora.

"We head for the council chambers. Once there we will present the evidence of Kolya's duplicity to the high priests."

"That may be easier said than done." Narim spoke quietly. "The number of Kolya's men in the city has been doubled in the past day. Kolya and Braen are planning something; I think they intend to overthrow the council. There are as many Genii guarding the council as there are Irithian guards. It will be difficult for us to gain access. I suggest we avoid the direct route to the council chambers."

Narim led them through corridors into a part of the city that had a utilitarian air far removed from the grandeur Rodney had seen nearer the entrance. Once they reached a large open room which served as a meeting place for five different corridors he stopped. Directing Rodney and Peran to a small, half hidden alcove, he told them to wait while he and Sora went on ahead.

"We shall be back shortly. Watch in that direction." he pointed to where a wide walkway joined the room. "If you spot any trouble come after us." Both he and Sora were gone before Rodney could ask what exactly they thought constituted trouble.

ooOoo

Waking up was painful. The shadow over his left eye and the throbbing in his head suggested that the rifle butt had left him with one hell of a black eye. With his vision impaired, he sensed rather than saw the movement in the room; he knew who it was.

"I am sorry. Benedict is not a soldier; it was wrong to do what we did."

"Why McCormack?" His words came out slurred and almost inaudible but in the quiet cell the commander understood. "Why not me?"

"Kolya and Braen are enjoying your suffering too much." Iestyn looked at the floor. "But accidents happen, all it would take is for a beating to go too far and you could bleed to death in your cell. You would only have to say. I hope it never comes to that." John closed his eyes; he knew what Iestyn was offering and was appalled at himself for feeling such relief in knowing there would be an end.

"I'm so tired."

"I know. But we're not there yet." Iestyn scuffed his boot on the floor. "When you were taken it was just you. The others were left unharmed."

"They're still alive?" He breathed the words out, scared to believe them. Nothing made sense anymore. "Alive." He repeated the word as if it was strange to him. Anger flared in him and, rolling over, he looked up at Iestyn's impassive face. "You bastard!" John's voice was cold and steadier than it had been in sometime.

"It was my job to break you. I'm good at my job."

"You wanted me to trust you." John screwed his face up in disgust. "I did trust you." With effort he sat up and, using the wall, he got himself to his feet. It was difficult to look intimidating when you could barely stand but he drew himself up to his full height and took a step forward, anger filling his gut. Iestyn studied his face and smiled.

"I knew there was fire in you yet."

ooOoo

Rodney and Peran had only been standing there for a few minutes, but it had felt like an hour. Two guards had walked past and had cast suspicious glances their way; he'd nodded at them and attempted something like a smile though he suspected it looked more like a grimace. For a moment he thought they were going to question him but it seemed that, now he was this, far people just assumed they were supposed to be here. He wondered what was taking Sora and Narim so long; he had half expected to be in the middle of a run for your life type scenario by now instead of standing around twiddling his thumbs. Peran had not said a word in the time they had been here, his eyes had remained trained on the walkway and the room, watching every movement like a hawk. Rodney couldn't help feeling that the young Genii looked more suspect than even he did right now.

An abrupt voice close by him made him start. Out of the corner of his eye he could see a man, wearing the uniform Rodney now recognised as that of an Irithian officer, standing talking to a stocky fair-haired guard. The officer looked tired; he rubbed his forehead as if trying to ease a headache. Rodney could sympathise, he wasn't having a good day himself.

"Where is Benedict now?" McKay's head snapped up at the familiar name.

"He is being prepared. If we had taken him instead of Sheppard in the first place it would have saved us a great deal of trouble."

_Sheppard. _The name hit McKay like a gut punch, knocking the breath out of his lungs. He strained to hear the rest of the conversation over the pounding in his head.

"You are right. I would have done things this way from the start; the Patriarchs have let the Genii make all the decisions. You saw Kolya with him. It wasn't a military decision to take him, it was personal vengeance. But what is done is done. Take some food and water down to Sheppard; I doubt he will be able to eat it but take it anyway." Rodney hugged the wall but the commander stormed past.

Rodney couldn't believe his ears. His friend was alive; alive and somewhere close by. The second man, small and stocky, stepped down a corridor. Rodney looked at Peran then after the retreating figure of the guard. It only took him a moment's hesitation before he was heading after the short, stocky figure of the Irithian. Peran grabbed his arm.

"Where are you going?"

"To find my friend." He snapped round, fixing the Genii with a defiant glare, and Peran flinched backward in surprise. "Don't even try and stop me," he hissed. There was a look of uncertainty in the Genii's eyes and Rodney used that moment to shrug him off. "You concentrate on what you came here to do; maybe that way we might all stand a chance of getting out of here alive." Turning back to the retreating figure of the guard, he hurried after him.

The guard headed down a narrow corridor and then started descending down a long staircase. Things were decidedly dingier here, the walls slightly damp and the lighting duller; this was clearly an older part of the city and had been neglected for some years. He stopped as the guard entered a side room and returned carrying a plate and cup, before carrying on down another staircase. This was stupid; he knew that. He was alone in a hostile city with no way out if things went wrong but he wasn't going to leave Sheppard behind, not again. Besides, if there was one person who could help him get out of this ridiculous situation it was the Colonel. The two of them had a history of surviving the impossible, you could almost call it a talent.

Rodney followed the Irithian down another corridor and short flight of stairs, at the bottom of which the corridor turned off to the right. He peered around the corner as the guard approached a large steel door, nodding into a guard room off to one side. A second man stepped out and began unbolting the heavy door. McKay tiptoed slowly downward, trying to get as close as he could. Suddenly alarm bells rang out and he froze, panic spreading through his bones as the guards turned and looked right at him. There was a moment of eye contact and then they were barreling down the corridor toward him.

Rodney turned to run, but felt a hand grab his shoulder spinning him back around. Screwing up his face he prepared himself for the worst - instead he found a tray of food and a cup of water roughly shoved into his hands. His mouth fell open.

"Leave this to us Genii, you guard the prisoner." And, with that, the two Irithians ran up the stairs. Rodney stood there stunned, unable to believe his luck. He gave himself a mental kick for wasting precious time. Hurrying down the corridor, he peered in through the door to the guard room, the Irithian's stupidity confirmed when he found it empty. Standing the plate and cup down, he drew back the last bolt on the cell block door and, pulling it half way back, squeezed through. He was faced with eight doors, four on either side. He stepped nervously along the corridor, listening for any signs of life. Taking a deep calming breath, he called out softly.

"Sheppard?" Nothing. He risked raising his voice a little more. "Sheppard?" He walked a little further down the block. "Sheppard, you here?" Hearing movement in the cell next to him, he took a step closer. "Sheppard, is that you?"

A bloodied hand shot out through the slot in the bottom of the door, seizing hold of Rodney's ankle with an iron grip. Screaming, struggling to break free, he lost his balance and fell, landing heavily on his backside. Still he desperately tried to wriggle free but the hand stayed attached to his ankle. Panicking he drew up his other leg, aiming his boot at the hand, bracing himself to bring his foot down with as much force as possible.

That's when he noticed the black sweatband and at the last second he forced his leg wide and the heavy boot just glanced the side of the hand, knocking its grip loose but not enough for it to let go. He stopped struggling and stared at the arm sticking out from under the door, a smile spreading across his face; he only knew of one person in the Pegasus Galaxy who wore a wristband like that. "Sheppard?"

"You scream like a girl, McKay." The voice was hoarse, little more than a whisper and even more slurred than Sheppard's usual lazy drawl; if it wasn't for the insult he'd have doubted who it belonged to. The scientist found himself giggling uncontrollably with a mixture of adrenalin and relief. "Open the God damned door." He felt the grip slowly release.

"Yes, yes of course, the door, hang on." Scrambling to his feet, trying to compose himself, he took hold of the large bolt and braced himself to draw it across. He couldn't get it to budge so he turned around to push it from the other direction. He was now facing the entrance to the cell block and at the doorway stood four armed guards pointing their weapons straight at him. "Oh crap!" He raised his hands in surrender just as Kolya walked into view.

"Doctor McKay! How lovely to see you again."

ooOoo

John felt as if his heart stopped at the sound of Kolya's voice. Footsteps tramped down the corridor and he watched as booted feet surrounded McKay and dragged him away. Rolling over, he lay on his back and stared into the blackness of the cell. Numb. There was no other word for it. Now he just wanted a swift end to it all. He lay there for several minutes, the hollow feeling inside threatening to consume him, before the latches on his cell door were pulled back. The dull glow of the electric lighting fell across him as the door was opened and he looked up into Iestyn's face, the commander's expression one of tired resignation. Opening his hand, Iestyn showed him the syringe.

"Is it time?"

Iestyn nodded. "Yes."

"I'm ready."


	12. Falling Down

_A/N - Thank you once again to everyone who went to the trouble of leaving feedback, I'm sure I don't have to tell the writers among you just how much it's appreciated_.  
_And thank you to everyone on the Shep whump thread at Gateworld for their encouragement when I was feeling disheartened - you know who you are._

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**Chapter 11**

**Falling Down**

Rodney was frog-marched down the corridor and back up the stairs. Kolya walked just behind him but, even without looking, McKay could sense the self-satisfied smile on the man's face.

"Do not worry, we're bringing Sheppard too, it's really going to be a very touching reunion." Rodney was pushed forward into a cell and forced to his knees. Three armed guards stood in the room, two Genii and the dark haired Irithian commander he had seen earlier; and out of the corner of his eye he could see two more Genii guards taking up position outside the door. Kolya smiled at him, clearly amused; Rodney met his gaze and held it. He'd been through terrified and had come out on the other side, now he was just seriously pissed off. He knew he was helpless here; this wasn't his thing, there wasn't anything he could think his way out of. He just had to hope that Sora and Narim would be successful.

Hearing movement in the corridor he looked up; the two Genii guards at the door parted and Sheppard was dragged in. Any vestige of hope Rodney had left him when he saw his friend.

ooOoo

Waiting. It sometimes seemed to Elizabeth that her life consisted of waiting. She longed to be doing something, anything, but all the decisions had been made and the plans put into action and all there was left to do was wait. When they had staggered back through the gate, exhausted and bruised, Caldwell had shown great restraint in not shouting 'I told you so'. But at least now they knew, they knew who had was responsible for the attacks and the thought of Kolya made Elizabeth's blood run cold.

"Unscheduled off world activation!" It was as if the whole city tensed at the words; perhaps the waiting was over. Elizabeth stood up, surprised at her own calm, and walked out to the control room.

"Are we getting an IDC?"

"Yes, ma'am." The gate technician turned to look at her, anxiety written on his face. "It's Dr Benedict's." All eyes were turned to her; this was her call. Her rational mind told her this was a trap but she also knew that there was a chance Sora had come good on her promise. If this really was Benedict she couldn't risk leaving the shield up, she couldn't kill an innocent man. Some people called her compassion a weakness but it was an inherent part of who she was and she hoped she'd never become so jaded as to lose it.

"Any radio contact?"

"No." She paused for the briefest moment, taking the time to look down at the heavily armoured marines down in the gate room, their weapons already trained at the event horizon.

"Open the shield. But if anyone other than Benedict, McCormack or McKay comes through it, you shut it down without hesitation." The soldiers focused entirely on the gate, ready to do what was necessary. "Do it."

The seconds that passed after the gate had opened stretched out into silence. When the figure finally stepped through, Elizabeth felt the breath catch in her throat; whatever she had expected, this wasn't it. Benedict stumbled through the gate, horror etched on his face; the words came tumbling from his mouth.

"I'm sorry." His eyes sought out Elizabeth's. "I'm so sorry…forgive me…I…I didn't know." A sob racked his body as he looked down at the explosives wrapped around his chest. "Please help me!"

Elizabeth screamed out at the stunned gate technician. "Raise the shield…" But her words never reached his ears.

The explosion was almost surreal. Elizabeth was knocked backward by the blast. After the crack of the initial detonation, a thick silence seemed to fall. Elizabeth opened her eyes and saw thousands of dust motes floating down through the air. She watched them falling gently as if time had slowed down; there was a strange kind of beauty to it.

Sound rushed back into the world and time speeded up, screaming, shouting, gunfire. Rolling on to her side and looking down at the gate through the dust filled air, Elizabeth saw figures swarming in through the wormhole like insects. Cries rang out from Atlantis' own soldiers; she couldn't see how many were injured from the explosion but she saw bodies littering the floor. More and more of the invaders entered the city until the whole of the gate room was filled with enemy soldiers.

ooOoo

Sheppard's thin frame slumped to the floor. His pale prison uniform was spattered with blood and at some point his thick, dark hair had been cropped close to his head. One side of his face was swollen and bloody, the other showed signs of healing injuries, faint purple shadows on his pale skin. An angry wound on his head looked fresh and, as his head lolled forward, Rodney could see a second blood-matted scar on his crown. Sheppard's arms, bound in front of him, were black with bruising and around his bonds were open sores, evidence of previous binds. One of his hands was swollen so badly it made Rodney wince just to look at it and he felt bile rising in his stomach.

"Oh my God! What have you done to him? Sheppard?" He got no response; his friend's eyes looked through him empty - dead.

"Don't expect an answer. I really don't think he's with us anymore. Such a shame." In a sudden movement, Kolya kicked Sheppard in the back, sending him sprawling across the floor. To Rodney's dismay, Sheppard didn't even try to protect himself and the impact with the cold stone floor opened up the wound on his forehead; a trickle of blood ran down his face as the guard hauled him up. As the Colonel's dark eyes passed over him he thought he saw a flicker of recognition but the vacant stare returned and he was left wondering if it was his own wishful thinking.

Out of the corner of his eye, Rodney saw a Genii soldier enter the room and hand Kolya a note. Reading it the conceited smile on Genii commander's face grew even wider.

"Our invading force should take Atlantis quickly. No doubt there will be a few pockets of resistance but, as you've seen, we outnumber you. As soon as the city is secure, I shall take you back with me. You can say goodbye properly; after all, Colonel Sheppard might not believe Doctor Weir is actually dead this time unless he witnesses it for himself."

Rodney finally tore his eyes away from the stricken Colonel to look fully at Kolya. "They know you're coming, they'll never drop the shields for you."

"They already have." Rodney studied Kolya's expression, unsure. He found it hard to believe that Elizabeth would have been tricked so easily but at the same time the man in front of him seemed utterly confident in his statement.

"It won't do you any good; you won't be able to run the city properly. Your scientists are at least half a century behind us, if not more, and none of your people have the gene. You won't even be able to use half the technology, including the jumpers." The Irithian commander was watching the exchange carefully he noticed, his dark eyes studying the face of his Genii counterpart.

"That is where you are wrong." Kolya glanced uneasily as the Irithian commander spoke. "The Genii have found among their people those who carry the blood of the Ancestors. Is that not true, General Kolya?" McKay rolled his eyes.

"Gene therapy? You've developed your own gene therapy." McKay wagged his finger at Kolya as he filled in the blanks for himself. "And these people are part of an Ancient worship cult. You're manipulating them, setting yourselves up as…what? The children of the Gods?"

"That's enough. You are full of lies." Kolya's composure faltered and Rodney could see his mind working. He didn't want this Irithian here. "They try and twist the truth. All they have done since they arrived in our galaxy is deceive us; it was they who awakened the Wraith, it was he," he pointed at Sheppard, "who slaughtered my men in cold blood. But now the True Heirs of the Ancestors have come and they can no longer hide behind their lies. You have seen the relics activated in the temple."

"True Heirs? And I'm supposed you're one of these miracle workers, are you?" Rodney spat out. Taking a step forward, Kolya backhanded him across the face, anger burning in the Genii's eyes. Rodney tasted the metallic tang of blood in his mouth; he'd been tortured by Kolya before and had been disgusted by his own weakness, this time he wasn't going to give in so easy. He spat a mouthful of blood out onto the floor and turned back to the Genii, meeting his eyes. "It didn't work, did it?" he taunted. "You had the treatment and it didn't take, you weren't compatible with the gene." Rodney sneered at him; he was starting to enjoy himself. "So tell me, how does it feel to be genetically inferior?"

Kolya grabbed him around the neck. "Do you want to die now?" Strong fingers constricted around Rodney's throat, digging into his flesh. His own heartbeat throbbed in his ears and at first he thought he was hearing himself choking but then, as he saw Kolya's brow furrow and his grip relent, Rodney realised that it was in fact the sound of someone laughing. Dry and strangled perhaps but a laugh none the less. Kolya let go of his throat and turned; Sheppard's shoulders were gently shaking as he giggled to himself, he looked up at Kolya an expression of pure hatred smouldering in his eyes.

ooOoo

The gate room fell in a matter of seconds. The soldiers uninjured by the blast had been stunned enough that the enemy forces running through the gate overpowered them easily. All Elizabeth could do was watch as, one by one, her soldiers were forced to the ground and bound at gunpoint. The commanding officer of the Irithian force radioed through to his superiors, notifying them of the successful completion of 'stage one'. Within minutes a group of Genii guards stepped through the gate, at their head a stocky man in a simple tunic, behind him, cloaked and hooded, came a man and a woman.

The leader of this group smiled triumphantly at the scene, gazing around the room. Elizabeth could see his chest swelling with pride and his eyes surveying the city, her city, with avarice.

"Doctor Weir?" Scanning the control room, he picked her out, spitting out her name as if it were a curse. "I am Patriarch Anwir Braen. Atlantis is now under the control of the Irithian-Genii Alliance, order your forces to stand down and surrender."

"And if I don't?"

"Then we shall take it by force, and kill everyone in the city."

"Well, I'm sorry to disappoint you but that's not going to happen." The open mic on her earpiece, which lay concealed in the palm of her hand, conveyed the conversation to the secondary command centre deep in the base of the city, where Radek Zelenka took control of Atlantis.

ooOoo

Kolya approached Sheppard cautiously, the burning look in the Colonel's eyes clearly unnerving the Genii.

"What is so amusing, Colonel?"

"This." As Sheppard raised his bound hands, McKay saw the knife concealed between his palms slip down into his grip. Sheppard threw his weight against the blow, ramming the blade into Kolya's thigh as hard as he could and twisting the blade, before barrelling into the commander with his shoulder and knocking him to the floor. Wrenching the dagger back out and pushing himself up, he planted a knee against Kolya's chest, pinning him to the floor, and then pushed the tip of the blade against his throat.

The two Genii guards reached for their weapons but the Irithian was quicker, he drew his weapon and took both of them down, kicking one of the fallen men's weapons toward Rodney as he did so. The two Genii guards from outside ran into the cell; the first met the Irithian commander's elbow face on and was soon on the floor. As the second guard ran in behind him, Rodney grabbed the weapon from the floor and, pointing it toward the door, screwed up his face and shot wildly in the guard's general direction. On the third attempt the Genii went down just as the Irithian put a bullet in the head of the other guard.

Breathlessly, Rodney turned, the weapon he held tightly clamped between his fingers, and pointed it at the Irithian, his hands a lot steadier than he felt. The commander spoke briefly into his radio and then returned Rodney's gaze.

"What the hell is going on?"

"My name is Iestyn and I just saved your life. I would have thought you would be more grateful."

"You're helping us?"

"Who do you think gave him the knife?" They both turned to look at Sheppard. He still had Kolya pinned to the floor, the tip of the blade had pierced the skin of the Genii's throat and a slow trickle of blood ran down to the floor.

"We need him alive, John." The Irithian took a step forward.

"No." The word sounded dry and harsh. Sheppard pushed the blade deeper and the blood flowed quicker, running down the side of the Genii commander's neck. Kolya struggled to breathe, not wanting to make any movement that would increase the pressure of the blade on his throat.

"If I am to convince the council of his lies, I need him alive." The commander went to the door, beckoning for his two guards to enter. "Do not make me use force. I have no wish to hurt you any further." Sheppard's face screwed up as if in pain at the sheer force of will it was taking him not to kill the Genii where he lay. The other man laid a gentle hand on his shoulder. "He will be punished I promise you that."

Sheppard stared into the face of the man he had pinned to the floor. He released the pressure slightly and Kolya cautiously gasped for breath. There was a brief pause before Sheppard raised the knife above his head and drove it downward toward the bloody throat of the Genii. At the last moment the Irithian commander grabbed him, pulling the knife away and dragging Sheppard off Kolya and onto the floor beside him. Sheppard screamed, a primal, inhuman sound, struggling against the Irithian and desperately grasping for the knife.

Kolya pushed himself backward up against the wall, trailing blood across the floor, and then turned, trying to make for the door, only to find himself confronted by two Irithian guards. McKay scrambled across the floor to where Sheppard still struggled weakly and took Iestyn's place holding the man down. The Irithian jumped to his feet and turned his attention to his new prisoner.

"Traitor! Braen will have you executed for this, Iestyn." Kolya spat out as the guards dragged him to his feet and bound his hands.

"Perhaps."

"Why?"

The Irithian glanced back at Sheppard.

"When you torture someone, you get to see who they really are." He looked back at the Genii and fixed him with a winning smile. "I shall look forward to getting to know you better, Acastus."

Rodney watched as Kolya was dragged from the room, leaving a trail of blood behind him. Once the Genii was out of sight, he felt Sheppard relax in his arms as if a spell had been broken. "Sheppard? You okay?" The Colonel's head bowed and his hands dropped so they lay between his knees. Releasing him and moving round carefully, attempting to make eye contact, Rodney took Sheppard's hands and, picking up the discarded knife, cut through the bonds, wincing at the sight of the open wounds around the other man's wrists and the swollen purple fingers on his left hand.

"Their feet are too small."

"What?" He raised his head at the sound of the quiet voice and followed the Colonel's eyes to the bodies of the two Genii guards. "Their feet?"

"Do you think they all have tiny little feet like that?" McKay closed his eyes and took a deep breath.

"You know, I'm having the day from hell and it would really help if you could not be crazy right now." Sheppard turned to him as if he'd only just noticed his presence, a distant, confused expression underlined with annoyance on his face.

"He does not have any boots, theirs are too small." Iestyn explained as he walked back in the door, wiping blood from his hands.

"Oh, right, of course." He looked at the Colonel apologetically. "Not crazy then, that's good." But he wasn't convinced. Sheppard still stared at him with the same strange look on his face.

"McKay?" Sheppard's reached up with his good hand and prodded the scientist in the shoulder as if checking to see if he was real. "Are you dead?"

"I don't think so but the way my day is going, it may only be a matter of time."

"He will be rather disorientated," Iestyn explained. "I have injected him with something for the pain and something to keep him awake but he still has other toxins in his system, so do not expect too much from him." Rodney looked at Sheppard, hoping that his friend was still in there somewhere.

"Are we going home now?" The softness in his voice and the look of hope in his eyes were childlike. Rodney wasn't used to this; Sheppard was the strong one. He forced a smile and patted the Colonel's arm gently.

"I really hope so."


	13. Lockdown

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_A/N - Thank you so much for the positive response to the last chapter, I couldn't leave poor Shep alone forever. I'm afraid I can't keep up the excitement levels of the last few chapters but I hope you'll all stick with me.  
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**Chapter 12**

**Lockdown**

The panels in the control room darkened as the bulkhead doors came down, sealing off the gate room from the rest of the city. Shouts came from the Irithian force as they tried in vain to prevent them closing. The Patriarch looked around, his overwhelming confidence slipping slightly. Returning his gaze to Elizabeth he shouted out above the lockdown alarm.

"You are foolish if you think you can stop us, Doctor Weir. You have just forfeited the lives of everyone in this room." Elizabeth's stomach tightened; if anyone was going to get them out of this now, it was her. It's why she had insisted on staying by the gate despite Lorne's determination to keep her as far away from danger as possible. Now he would be deep in the recesses of the city with Zelenka; if she should fall it would be his responsibility to defend Atlantis.

"I am not trying to trick you, Patriarch, I simply wish to negotiate better terms for my people."

"Negotiate?" Turning to his companions, he smiled as if she had made a joke. "Doctor, you have nothing to bargain with. I assume that whoever you have controlling the city can hear us now? Well they had better hear this; if control is not handed over to us we will begin to kill the hostages in this room, one by one, until you do; and they will not die quickly, we shall make sure their deaths are slow and painful, their screams will be heard throughout the city."

Elizabeth tried not to let emotion show on her face but she worried that she had misjudged the situation. She had been told that these people were religious, followers of the Ancients, but this man showed no signs of a compassionate religious leader; when he talked of killing and torture there was a note of glee in his voice. But she felt hope in seeing the uneasy faces of his companions.

"My men are prepared for that eventuality, they will not relinquish the city to you regardless of your tactics. All of us here knew the risk in staying by the gate." She took a step toward the staircase, her voice still calm even though she didn't feel it. "Patriarch, we could make this far easier on all of us if you will just be prepared to negotiate terms." Walking down the steps, she kept eye contact with him and felt a brief surge of triumph when he looked away.

The hooded man reached forward, placing a hand on Braen's shoulder.

"Let us hear what she has to say." Elizabeth bowed her head slightly to the man.

"Thank you, it would be a shame to see unnecessary blood shed in the halls of the City of the Ancestors." Appealing to their religious beliefs was a risky business, they could easily take offence, but she felt it was worth the gamble. All she had to do now was stall them.

ooOoo

They headed down the corridor after Iestyn, leaving a shoeless Irithian guard behind. McKay kept by Sheppard's side; he was unsteady on his feet though Rodney found the fact he was able to stand at all amazing in itself.

"Wait!" Rodney called after Iestyn. "What about McCormack and Benedict? You have two more of our people."

"They are both dead."

"McCormack made a mess." Rodney turned to see Sheppard holding out his shirt, examining the blood stains. He slowly raised his eyes, pain and confusion etched on his face. Rodney swallowed back hard, pushing down the rising sense of horror.

"What did they do to you?" he whispered.

"He will recover." Rodney turned on Iestyn.

"He'd better." Rodney gently took hold of his friends arm. "Where are you taking us?"

"There is a lower level of the city that lies abandoned. I will show you how to reach it, from there I will tell you how to find an exit out on to the planet surface. From there you are on your own, I'm sorry there is nothing more I can do. If, once this is over, I can help you return home I will find you but I make no promises."

"Run and hide?"

"Neither of you is fit to do anything else." Rodney looked at Sheppard whose eyes had once more glazed over. "The best you can do now is protect your friend." Iestyn looked away, anger burning in his eyes. "There will be fighting, it seems your city is not the only one the Genii want." He turned back to Rodney with a rueful smile. "Now please hurry, my place is with my people."

ooOoo

Elizabeth held firm. "We only ask that our civilians be spared, there is a settlement on the mainland. We wish to relocate there, all we ask is to be allowed to live in peace." Braen eyed her suspiciously but the senior priest and priestess were prepared to hear what she had to say. Glahan was a small, portly man and under other circumstances she would have found him almost comical; in total contrast the woman, Arlais, was tall and elegant and seemed almost ethereal; her hair was a perfect silver, her skin like ivory and her eyes a piercing pale grey.

"And what of your military personnel?" Glahan asked.

"It would be understandable if you would wish to keep them as prisoners but in time I would hope that you would allow them to join us. Once you hold the city and our weapons, you would have little to fear from us."

"I have heard much of you, Doctor, and I find it hard to believe that a woman such as yourself would cede defeat so easily."

"We did not come to this galaxy to fight wars, my Lord Patriarch, we came to explore, to make new allies. It is a shame that you did not seek dialogue with us before, it would have saved the lives of innocent men and women on both sides." She deliberately tried to echo the priest's way of speech.

Braen stepped forward, placing his hand on the other man's chest. "Do not listen to her, they are liars and deceivers. You heard what Kolya said, she will try to manipulate you. Do not be led astray by her untruths."

"Remove your hand from me." His voice was cold and Braen shrank back at the sound of it but Elizabeth could see anger boiling inside of him. "Is there anything you are keeping from us, Doctor?"

"I have only one request. We shall need some form of transportation; we ask that we be given four of the ships we call puddle jumpers. After all, they will be of no use to you as none of your people can fly one."

"Among the Genii there are those that can awaken the technology of the Ancestors, as well you know." Elizabeth nodded. That explained a lot; Laden Radim's gene therapy experiments had come to fruition.

"I didn't know that, actually, but it is interesting to learn."

"More lies my Lord, we should kill her now, before she poisons our thoughts any further."

"SILENCE!" The voice of the Lord Patriarch roared. "The council has given you free reign over this for long enough and I have supported you but I will not be told what to think by you any more than her."

Braen bowed his head. "My apologies. I only wish what is best for our people."

"Then you shall hold until I have spoken with the rest of the council. If I find you have harmed any of these people without my express order, you shall suffer the consequences. Remember your place." Braen bowed again but, as he lowered his head, Elizabeth couldn't help but notice the scowl of hatred that passed across his face. This was an ambitious man just awaiting his moment.

ooOoo

Iestyn led them out of the cell block and toward the guard house. On seeing him one of his men ran over to report.

"The Genii have control of both the gate and the council chambers, Sir. And some of our own troops have joined them."

"Patriarch Braen's men. Return to your post, I shall be there shortly." After dismissing the guard, Iestyn turned back to Rodney. "See this corridor? Follow it to its end; there you will find a door." He took a piece of paper from his pocket and scribbled down some symbols before handing it over to the scientist. "This is the code to unlock it. Once on the other side, you will find a service hatch to the lower level, it has been abandoned for many years. Follow the main street until its end, there you will find another guard house far grander than this one. Inside there is a staircase leading to the outside. This entrance is long forgotten and only accessible from the inside so shall not be guarded. There should be torches near the hatch, you will need them." Suddenly, gunshots rang out behind them. Iestyn grabbed Rodney and shoved him toward the corridor. "Go now!" The Irithian drew his weapon and headed to join his men.

Grabbing hold of the still incoherent Colonel, Rodney dragged him down the corridor, eager to leave the sound of weapons fire behind. When they reached the door he held up the piece of paper and hurriedly entered the code. Hearing a quiet thump behind him, he turned to see Sheppard sliding down the wall and slumping onto the floor. Bending down, he gently tapped the pilot on the side of the face, half scared of hurting him.

"Hey Sheppard! Sheppard, you still with me?" Hazel eyes forced themselves open.

"Still here," he mumbled.

"Then help me get you on your feet again." Crouching down, he pulled Sheppard's arm around his shoulders. "How can someone so skinny weigh so much?" As he braced himself and pushed upward, Sheppard let out a small cry of pain. "Sorry! Drugs wearing off, huh?" That was one more thing for Rodney to worry about. As soon as they were both through the door he slammed it shut, deadening the sound of gunfire on the other side.

The room they had entered was almost pitch black. From the brief glimpse he'd got before slamming shut the door, Rodney managed to fumble his way across to the rack of torches on the wall. He turned one on and saw Sheppard wince away from the light.

"Sorry!" He grabbed another torch and passed it to the Colonel.

The hatch on the floor had a large wheel lock on it. Sheppard rested against the door post, looking out into the dark with a sad, far away look on his face while McKay struggled to undo the rusted hatch; he rambled, a nervous habit and right now he felt he had every call to be nervous.

"I'm not cut out for this. I'm supposed to be in a nice safe laboratory, coming up with dazzling new discoveries, winning Nobel Prizes, getting international acclaim…no wait…intergalactic acclaim. Then we'd see who'd get all the girls." He was startled and somewhat relieved to hear Sheppard chuckle. "Oh yeah, that's it go ahead and laugh." The wheel suddenly started to give, screeching as it turned, and they both winced at the noise. "I'm telling you, a lot of women find a brilliant mind an extremely attractive attribute in a man. Those boyish good looks of yours won't last forever you know." The Colonel walked over to him and into the light from the torch; looking up, Rodney saw his friend's gaunt features, bruised and bloodied almost beyond recognition, and had to look away. Hoping that Sheppard hadn't caught the expression on his face, he dragged the hatch open and looked down the shaft underneath.

"Oh crap!" The ladder reached down into blackness. He looked back up at the Colonel. "Can you do this?"

"No choice."

Rodney nodded, relieved to be getting a coherent response. "No, I guess not. Should I go first? You know, in case you fall or something."

"S'okay." Rodney watched as Sheppard slowly and painfully eased himself on to the ladder, his broken hand held against his chest and the other wrapped around the ladder so he could slide it down as he descended. Rodney found himself holding his breath as he watched him take the first few steps. As soon as Sheppard was far enough down, Rodney swung himself out on to the ladder above him and pulled the hatch down over them, securing it with more ease than it had opened while holding the torch between his teeth.

Looking down, he saw Sheppard's torch bobbing about further down.

"You okay?"

"Spooky."

"What?" Rodney reached the bottom, finding Sheppard leaning against the wall, turning his torch this way and that. They were standing on an abandoned street; to either side of them buildings had been hollowed out of the rock, lamp posts that had long stood dark lined the street, faded signposts tilted on walls, doorways stood open like gaping mouths. An eerie, subterranean ghost town.

ooOoo

Among the Genii contingent of the invasion force were scientists who now worked trying to bring the consoles back to life. Elizabeth was confident it couldn't be done. Now the lockdown had been put in place, the only person who could override it was Zelenka. She had made sure that even her command codes wouldn't work, not prepared to risk the chance that she would give them up. The only other person who would be able to gain control of the city would be Rodney and he wasn't here. She thought back to Benedict, the look of utter terror and despair on the man's face, and tried to push her fear for the man who had gone to save him to the back of her mind.

Arlais and Glahan were standing in a huddle near the gate, a heated debate going on, though their voices remained hushed. Elizabeth studied the body language carefully; the two leaders were becoming agitated, clearly unhappy with what they were being told, while Braen stood off to one side, his body still and calm. Braen was the problem, she knew. The others were calculating, and she knew they would have no problem with using force if necessary, but in his eyes she could see a kind of madness, a lust for power. The conquering of Atlantis was his chance to achieve greatness and he wasn't going to let anyone stand in his way. His arrogance and power lust were his weaknesses.

Now they walked away from the gate, heading back toward Elizabeth. The voice of Lady Arlais, who up until now had remained silent, carried across the room. "Something is wrong."

Braen answered him. "My Lady, I see no reason to believe that. As the Genii Captain explained, the rest of the council has been taken to safety after intruders were discovered in the city. I am sure you will be able to speak with them soon." Intruders? Elizabeth tried not to betray any emotion on her face; it had to be Rodney and Sora.

"Then why could I not speak with any of our soldiers?"

"The Genii battalion is at the gate awaiting your orders; our own soldiers are busy elsewhere, protecting the council. If you would just be patient, my Lady, I am sure that they will soon have the situation under control. In the meantime, it is our job to secure Atlantis." A predatory smile crossed his face. "Shall I order the Genii battalion to come through the gate?" He moved, raising the radio ready to give the command.

"No." Braen gritted his teeth as once again he was overruled. "They stay where they are, there is no point in them coming here until we have got these doors open. Why can the Heirs not open them? Surely they should have command over the city."

"They," he pointed accusingly at Elizabeth,. "have sabotaged the city, my Lady. Yet more sacrilege on their behalf; I say let us use force." Braen was barely containing his frustration. "We cannot allow them to delay us any longer, begin killing the prisoners until one of them breaks."

"And if that does not work?"

"It will. They are weak; Benedict crumbled at the sight of his companion's blood." Elizabeth closed her eyes. She now knew the fate of both of the Atlantean hostages. She tried to push back thoughts of Rodney; she couldn't let her mind be distracted from the task in hand. "We should kill the soldiers first; the civilians are more likely to break." The two High priests looked at each other in silent communication.

Glahan sighed and Arlais looked away. "Very well. Begin."


	14. Slow Motion

_A/N:- Sorry for the wait in updating but hopefully you'll get two chapters quite quickly now. I'm putting this up early in the morning so if there are any mistakes I apologise I'm still a bit sleepy. I hope you're still with me, only four more chapters and an epilogue to go after this one so we're on the home straight but it won't be all plain sailing. As always feedback is appreciated._

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**Chapter 13**

**Slow Motion**

Elizabeth darted forward and guns swung toward her as she did so, guards closing in around her, preventing her from reaching the priests. Glahan turned to look at her.

"Please, Lord Patriarch, I'm sure none of us want there to be anymore bloodshed. If you could just wait until you have spoken to your council." She needed more time, she didn't know how much but it couldn't be long now. Out of the corner of her eye she saw Braen pointing out a man in the group of prisoners and saw the guards drag Corporal Hines, a young marine, out in to the centre of the room, making sure that all the Atlanteans had a good view. "Please, I am begging you not to do this."

Glahan took a step toward her. "Then tell them to open the doors and surrender."

"They have been told to disregard any order I give them while I am held prisoner."

"Then we have no other choice." Turning back his back to her, he addressed Braen. "Can the others in the city hear us?"

"I believe they can hear us through this," He handed the earpiece over. Glahan turned back to Elizabeth.

"Is this true?"

"Yes." She admitted there had been an open com link between them and the control room the whole time and the priest examined the tiny earpiece in his hand before raising it to his mouth.

"Hear this. We are about to begin the execution of your people; everyone of them will die unless you relinquish control of the city to us." Lifting the communications device to his ear, he listened intently, frowning. "He speaks nonsense."

"Czech actually. Please may I speak with him?"

"No." The priest passed the earpiece back to Braen. "It is too late for talk, now we must finish what we have started." Braen smiled at her and it sent chills down her spine. He walked over to Hines, gesturing for the guards to push him to his knees. As soon as the solider was kneeling down the priest kicked him, knocking him over, and continued continued to kick at the defenceless man, Hines curling into a ball to try to protect himself. When the guards dragged him up on to his knees again, he stared up at the priest, making eye contact and setting his mouth in a defiant sneer.

"Are all your soldiers so foolish?"

ooOoo

They walked in silence for a while, both slightly in awe of their surroundings, until they came upon an open area, a large court yard centred around a now dry fountain. Mosaics were set into the paving and benches were set in a circle around the perimeter of the courtyard. In the dark, the strange statues of some kind of animal that formed the fountain looked like something from a horror film and the whole area felt creepy but they were in need of rest. They lowered themselves down onto one of the benches and sat silently in the dark, preserving the batteries on the flashlight As Sheppard had become more coherent, the agony written on his face had become more obvious, McKay knew that whatever Iestyn had given him was wearing off and that the pain was only going to get worse for him. Unable to bear it any longer, Rodney broke the silence.

"I'm sorry."

Quizzical eyes turned toward him. "What for?" Sheppard's voice was still slurred.

"We left you behind."

"No…you came and found me." McKay cringed.

"No, I didn't. I was kidnapped by Sora and forced to come here and we were looking for Benedict and McCormack, not you. I didn't know you were here." In the dark he couldn't quite make out the expression on his friend's face.

"We need to keep moving." Sheppard stood up and began making his slow way through the dark. Rodney watched his friend's painful movements from the bench, his heart sinking. As the Colonel stumbled, he dashedforward, not quite managing to catch him in time. Sheppard stumbled to the floor, letting out a harsh cry that echoed through the empty streets. By the time Rodney was at his side, he had rolled over onto his back and was panting in sharp breaths.

"Are you okay? Stupid question, of course you're not okay. You need to rest more."

"I'm good."

"No. No, you're not for God's sake." Sheppard's good hand reached up and took hold of Rodney's collar.

"I need to get out. I won't lay down and die in the dark Rodney." Rodney sat back on the ground beside him.

"Good. Because you are not allowed to die now, that would be the most selfish thing you've ever done - I would stand a chance here on my own." Rodney rubbed his temples. "But say we get out of here, reach the surface, then what? If Atlantis is really under attack they won't have come looking for us; there'll be no Daedalus waiting for us. And it's not like we're going to be able to fight our way through a battalion of Genii soldiers to get to the gate. We're stuck here and you need a doctor and you're gonna die and leave me on my own."

"They told me you were dead, you know?" His voice was little more than a whisper. "You, Ronon, Teyla, Elizabeth…all dead."

"Well, obviously we're not…at least I'm not," he added quietly. "And the others weren't last time I saw them. Though Ronon was trying to take on an entire bar full of drunks." Sheppard furrowed his brow. "Long story."

"Anyway my point is…if they lied about you, they could have lied about Atlantis." Rodney could see in his face that Sheppard didn't really believe it but knew what he was trying to do.

"Only you could be optimistic at a time like this."

"One of us has to be."

"Well, forgive me for being a little more realistic. We're stuck in the dark in an abandoned section of an alien city, underneath a mountain, on a hostile planet; our home is being invaded and there's nothing we can do about it, you're falling apart and I'm exhausted, my face and my neck really hurt and to top it all I don't remember the last time I actually ate anything!"

"It's called hope, McKay. Seems they didn't quite beat that out of me after all." He paused for a moment. "We're underneath a mountain?"

"You know, I would have thought that us being in a massive cavern with buildings carved out of the rock might have been a clue."

"Cool!" Rodney rolled his eyes. "McKay?"

"Yes." His voice was a little harsher then he'd intended.

"Help?" He looked at the Colonel still laying flat on his back.

"Sure." It was an awkward manoeuvre and Rodney felt his friend's body tense as he levered him up. Sheppard let out a sharp hiss of breath and a muffled whimper. Even here, with just the two of them, he wouldn't let go and show just how much pain he was in, though in the soft glow of the torch light Rodney could see the sheen of tears in Sheppard's eyes. He looked away, filling the silence with the first thing that came into his head.

"They replaced you on the team." He winced. Tactlessness wasn't something he did intentionally, it just kind of happened.

"Yeah?" He spoke through gritted teeth.

"Her name's Izzy." Sheppard stopped and turned his good eye to McKay, squinting suspiciously at him.

"Let me guess, she's blonde."

"Well…yes, as a matter of fact, she is." He paused, smiling smugly. "I think she likes me." Sheppard gave him an incredulous look. "No…really, she brought me pastry."

"Oh! Well in that case it must be love."

ooOoo

Elizabeth never got a chance to answer; the flash of white light was blinding and was followed by a second and then a third. The Irithians looked around in shock and fear, raising their rifles, unsure where to aim. At the same time the blast doors opened and Lorne led the Atlantean forces into the gate room, using the panic to disarm the Irithians nearest to them.

Two groups of heavily armed marines had beamed in and now stood in front of the gate, Colonel Caldwell standing at their front, P-90 firmly in his grip, while at the base of the steps just in front of Elizabeth, Ronon, Teyla and Frischmann appeared flanking a small guard of Genii at the centre of which stood Ladon Radim.

Elizabeth breathed out heavily. "I never had you down as a showman, Colonel, but you certainly know how to make an entrance."

"Thank you, Doctor. It's all in the timing." Elizabeth allowed herself a smile of relief.

"Ladon, thank you for coming." He bowed his head toward her.

"What is the meaning of this?" Braen bellowed, staring around in shock. The invading force were surrounded and each side now held their weapons trained on the other; a single shot fired would begin a bloody fire fight. Now it was up to Elizabeth to stop that from happening.

"This is called diplomacy, Patriarch, a concept you seem to have trouble with." She turned her back on him and concentrated on the two senior priests. "This is Ladon Radim, leader of the Genii people."

Ladon stepped forward, bowing to the two priests. "It is an honour to meet you."

Braen barged in between them, his face red with fury. "Lies! Lies and tricks, we will not listen to them." Ronon's hand was suddenly resting on the man's chest, stopping him dead in his tracks. The Satedan looked at him raising an eyebrow slightly.

"Braen, you're surrounded by my forces. I really don't see right now that you have much of a choice," Elizabeth pointed out to him.

"We could shoot our way out." Even he didn't sound convinced.

"Go ahead and try." Elizabeth was back in control and she wasn't going to show an inch of weakness; if this madman did give the order to start shooting then it would be horrific, she had to just trust that his soldiers wouldn't be so stupid. Arlais stepped forward, pushing Braen out of the way.

"You fool! You have walked us into their trap with your arrogance."

Elizabeth kept her tone of voice calm and precise; with so much panic and confusion it was important that she remained the voice of reason. "Lady Arlais, this is not a trap. I wish to make peace with your people. Please, listen to what Ladon has to say."

"And how are we to know that this is truly Ladon Radim?" Ladon stepped forward and pointed out the Genii working on the consoles.

"Ask them, they will tell you who I am." He called out to them. "Or will you continue your treason by denying your leader?" The Genii scientists looked to one another, their faces a mixture of fear and anger.

"No, Sir."

"Good." He turned back to the priests. "Satisfied?"

"What is happening here?"

"These people their not your enemy. Kolya has manipulated you and, while you and a large proportion of your forces stand here, he and his army are invading your city." There was a ripple of murmurs through the Irithian forces and the Genii huddled closer together.

"Lies, more lies. He is conspiring with the heretics," Braen called out, once again pushing himself forward and once again coming into contact with Ronon's hand.

"Well, you'd know all about conspiring, wouldn't you Braen?" Ladon stepped forward and began circling Braen. "Ask yourselves, who has been working so very closely with Kolya? Who has pushed this plan of action from the start? Who insisted that it was safe for members of the council to be among the invading forces?" Never taking his eyes off Braen, he continued to speak to the other two men. "If you do not believe me, send a soldier through the gate and see if he returns; the Genii holding the gate will shoot him on sight."

There was silence; the two priests looked to be in shock and the soldiers on both sides stood rigid with tension, fingers hovering over triggers. Elizabeth stepped forward.

"Please, tell your men to stand down. We can end this peacefully."

"If what he says is true, our city is under attack, how can it end peacefully?" Glahan asked, his voice quiet and sad.

"They are lying, my Lord!" Braen screamed out, his face slick with sweat, anger burning in his eyes.

"SILENCE! What did they offer you? What could make you turn on your own people?" Glahan demanded. "I knew you always craved power but to sink to such lows. You disgust me!"

"They offered him the gene therapy," Ladon provided. "Those Genii you call the Children of the Ancestors, or the Heirs, they only have the ability to operate the technology of the Ancestors because of a medical procedure which my scientists developed using samples taken from Doctor Weir's people."

Glahan and Arlais looked at Elizabeth, confused. "You are the Children of the Ancestors?" The man asked.

"No. At least I'm not, but there are those among my people who I guess could claim that title." An image of John sitting in the chair in Antarctica crossed her mind but she pushed it away. "Now please, tell your men to stand down so we can try and find a solution to this mess. I promise you they will not be harmed."

Holding out her finger, Arlais pointed at Braen. "I ask for no such promise regarding him." Turning to face her men, she called out. "Stand down! Surrender your weapons and give no resistance."

Almost as one the Irithian guards dropped their weapons and Elizabeth could have sworn she felt a cool breeze pass through the gate room, almost as if the city itself had sighed with relief. She grabbed the earpiece Frischmann held out to her.

"Carson, I want a medical team in here straight away; multiple serious injuries."

"Already on my way." The Scot's voice came back over the radio.

"Radek, return control of the city to the main control room and get up here."

Arlais and Glahan hung their heads as a sign of submission and held out their wrists to Teyla and Frischmann. The Captain creased her brow and looked to Elizabeth with a shrug.

"I don't think restraints will be necessary do you, Doctor Weir?"

"No. Certainly not. Now please let me show you to the conference room; we have a lot to talk about and not much time."

ooOoo

John was shivering again; this deep empty part of the mountain was freezing and all he had on was his thin prison tunic and trousers. McKay walked beside him, watching him like a hawk, the slightest stumble and the scientist was there to grab hold of him. It wasn't that he didn't appreciate it, it's just that it made him feel all the more useless. They must nearly be there by now, assuming they hadn't lost their way in the dark.

The painkillers Iestyn had pumped him full of were still having some effect; now the drugs were just making him clumsy and slow-witted. When he got home he was going to let Carson dope him up with as much morphine as he liked. He'd stay in the infirmary for a month if the Scot asked him to, he just wanted to be home and free of pain.

In the faint light of the flashlight, he could just make out McKay's features; he had that determined look on his face and he hadn't moaned about the walking in at least two minutes which was pretty impressive, considering. Who'd have thought he could have grieved so much for that smug face and annoying whiny voice?

"Kinda missed you…just a little bit." McKay bobbed his head slightly but kept looking straight ahead.

"Yeah, kinda missed you too…every now and then." The scientist hesitated, swallowing back. "We never gave up looking for you, you know that right? We didn't know where you were."

"I know, it's just…" His voice cracked and the words drifted away. "It's okay." He forced a smile, McKay returned it half-heartedly, and they continued their long trudge through the dark.

ooOoo

Now that the priests had time to take in the city, they looked at everything with wonder. Elizabeth had guided them to the conference room along with Ladon; she treated all three of them as she would honoured guests but Ronon, Teyla and Frischmann stood guard, their hands on their weapons and eyes alert. Caldwell joined them at the table while Lorne dealt with the surrendered soldiers, being sure to keep the Irithian and Genii separate from one another. Elizabeth took her seat at the head of the table.

"Gentlemen, as I said, time is of the essence so we need to move quickly. It appears we are all victims of the same lies. Kolya has caused a civil war among the Genii, forcing Ladon into hiding," She nodded at the dark haired man who turned his eyes away, a hint of shame on his face. Sora had been right; Ladon was weak. He was undoubtedly highly intelligent but he lacked the strength for leadership. "while the Irithian people have been manipulated into a holy war and then turned on by their allies. If what Ladon's spies tell him is true, it is not safe for you to return through the stargate if the Genii hold the other side and, based on your conversation earlier, I am assuming that is the case."

Arlais nodded ruefully. "It would appear so."

"So, we need to find another way." Elizabeth nodded toward Steven Caldwell. "Colonel."

Caldwell leaned forward. "We have a ship capable of transporting your people back to your planet within a couple of hours, we can then transport them down to the surface in the same way you saw myself arrive with my men. We can't fit all of your men on board, and we'll have to put them down outside of the area of your jamming field, but there is space for a sizable strike force, and with the added benefit of surprise you should be able to retake the gate."

"Why would you do this after everything we have done?" Arlais asked.

"Because we're not like Kolya." Elizabeth answered simply. There was anger at these men, she could feel it inside her and sense it in the soldiers outside, in the other Atlanteans in the room, but she also felt sorry for them; their faith and belief had been turned against them. "I won't pretend that our people can be friends anytime soon but I know that you would not have carried out your attacks on my people without Kolya's intervention and I will not send you back through that gate to certain death."

"Then we accept your more than kind offer. If we could please speak with our officers?"

"Of course, but Ronon and Captain Frischmann will stand guard."

Getting up, she left the conference room and headed for her office, gesturing for Caldwell and Teyla to follow her. Stopping on the balcony, she looked down at the scene in the gate room; Lorne had begun moving groups to the holding cells, beginning with the Genii. Half a dozen stretchers lay out on the floor and Carson was working furiously on one soldier, shouting out instructions to his staff. Another group of medics crouched down over another marine; his shirt had been cut open and they were charging the defibrillator. Her skin crawled at the sight and her own body jumped as the marine's body jerked with the electric pulse from the paddles.

Walking into her office, she wrapped her arms around herself and rested her head against the glass, looking down at the chaos below. Feeling a hand on her shoulder, she turned to see Teyla's worried face beside her.

"Elizabeth?" She forced a smile.

"I'll be okay." Turning away from the window, she took a seat perched on the edge of her desk.

"Are you sure you're okay with this, Colonel?"

"Honestly, no." Caldwell answered. "The idea of having a group of enemy soldiers on my ship isn't particularly appealing but you're right, we can't just send them back through the gate. The other option is we ferry them back in smaller groups, put them down further away from the city and let them fight their way in once they're all there."

"But that would give the Genii plenty of time to gain a strong foothold within the Irithian city." Teyla pointed out.

"Not really our problem."

"No, but finding Doctor McKay is. If they have been captured then it is in our best interests to help the Irithians."

"Teyla's right, Steven. This is the way we have to do things."

"You're the boss."

"Yes, I am. So get to it." Caldwell nodded and left the office, already talking to Hermiod on the radio.

"Ronon and I would like to go with the Daedalus, we have already lost one of our team, we would like to do what we can to find Rodney and bring him home safely." Elizabeth smiled, nodding sadly.

"Of course, take Frischmann too." Teyla inclined her head in a slight bow before leaving to inform her team mates. Elizabeth headed for the balcony; she knew it was selfish of her but she just needed some fresh air to clear her head, needed the stability offered by the familiar view of rolling waves stretching out into perfect blue. For a moment she lost herself in the vista only to be snapped out of it by Teyla's urgent voice in her earpiece.

"Doctor, come quickly! There is something you must hear." Elizabeth raced back into the control room in time to see Ronon dragging Braen toward the conference room by the scruff of his neck. The priest screamed abuse at the Satedan and Elizabeth could see the quiet anger raging inside the big man. Elizabeth ran after them and watched as, upon reaching the conference room, he threw the priest across the table.

"Ronon! What the hell do you think you're doing?"

"They have Sheppard." Elizabeth felt like the breath had been knocked out of her.

"What?" She looked questioningly at Glahan and Arlais.

"We are sorry, we thought you knew." Ronon had picked up Braen and was holding him by the neck up against the wall.

"No, we…he's alive?"

"I am afraid I do not know, I have never seen him; Braen always dealt with the prisoners." Elizabeth looked at the man Ronon held up against the wall, his face slowly turning purple and foam forming at his mouth.

"Ronon, put him down." The big man slid the priest down the wall so his feet touched the ground and released his grip enough for the man to breathe. "Is Colonel Sheppard still alive?"

The priest sneered triumphantly. "No. He's dead."

Elizabeth struggled to hold back her emotions. "You're sure?"

"Kolya killed him this morning; we had no further use for him, his mind was gone."

There was such delight in the man's voice. He got a kick out of seeing their pain, it was one little piece of power he had left. When Ronon smacked the man's head back into the wall it took all of her strength to tell him to stop. The Satedan ignored her, still holding the man gripped round the throat.

"Ronon, please! This is not the way." She looked at Teyla for help and could see anger and disgust burning in her normally gentle eyes. Elizabeth could see the effort it took for her to softly prise Ronon away from Braen who slumped to the floor as he was released. Teyla looked at him with disgust as she held tightly to Ronon's arm.

"Ronon, let us try to find Rodney and bring him home safely. That is what John would want us to do."


	15. Lost & Found

_A/N:- As always many thanks to those of you who took the time to leave feedback. Now here we go with another shiny new chapter._

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**Chapter 14**

**Lost and Found**

"Do you think this is it?" asked McKay. Sheppard just stared at the building, swaying slightly, pain written on his face. "Iestyn did say it was very ornate and I think this definitely qualifies." The building sat hollowed into the rock at the end of the wide main street, hewn in to its face were an array of figures; powerful warriors and curvaceous goddesses intertwined together. "It definitely stands out."

Whatever kind of power the flashlights ran on was running low and the light was slowly dimming. They had turned one of the flashlights off in order to preserve power and, viewed under the fading light, the carved figures took on an almost sinister air.

"Let's go take a look." Sheppard's voice was weak and strained. When Rodney went to take his arm, the Colonel didn't hesitate to except the help, leaning heavily on the shorter man, the relief on his face palpable. That in itself worried Rodney, the fact that Sheppard had given up trying to hide his pain, any pretence that he didn't need help had dissipated.

Sheppard's lucidity had improved dramatically; his speech was perhaps a little slower than usual, slurred and hesitant and his sentences shorter and there were often long periods of silence in-between. That wasn't unusual for the Colonel; he could be a man of few words at times, but sometimes walking through the dark it had almost seemed like he wasn't there at all - a ghost in a ghost town.

"What then?" That was the question; what would they do once they'd reached the outside? What could they do?

"We wait."

"And if they don't come?"

"Then I'm screwed."

"We both are," Rodney corrected him. It was that simple. If the Daedalus didn't come soon they were dead. Or at least Sheppard would be soon and the likelihood of an astrophysicist, no matter how brilliant, surviving in the wild for any length of time would be pretty low. Somehow Rodney couldn't imagine himself hunting down wild animals and gathering berries. There was this abandoned part of the city of course, but if the Genii succeeded in taking the Irithian city too then even these deserted streets would be scoured for anyone in hiding and would no longer be safe.

ooOoo

"I'm sorry, Doctor Weir, for everything. I never intended for any of this to happen."

"You should have come to me weeks ago, Ladon. I thought we had come to an arrangement; we have been giving you medical assistance for months, have saved the lives of hundreds of your people, and this is the thanks we get." The two of them stood alone in her office; Lieutenant Edison loitered outside the door watching the man carefully.

"This was Kolya's doing. I had…"

"Nothing to do with it? Yet you've known about it for weeks and did nothing. Did you know they had Colonel Sheppard?"

"No. I admit I suspected that Kolya might have had something to do with his disappearance but…"

"But you never even saw fit to tell us Kolya was still alive. When the Colonel first went missing we came to you and you swore you had nothing to do with it."

"I didn't."

"But you had a good idea who did and you never told us. You could have stopped innocent men and women dying and yet you did nothing."

"I helped you here today, I saved you." Ladon protested.

"We had to hunt you down to a planet where you were hiding from your own people, the same people you are supposed to be leading, and drag you here under threat of violence. Is it any wonder your people looked elsewhere for leadership? Get out of my city, Ladon, and take your people with you."

"Doctor Weir, I…" Elizabeth took a step closer to him; she kept her voice quiet but that only served to make her tone more threatening.

"I said, get the hell out of my city." Edison walked in the door and placed a hand on the Genii's shoulder.

"I think you should come with me, sir." Ladon shrugged the marine off and marched out of the room toward the gate, leaving Elizabeth alone, almost shaking with anger. She felt so powerless. Powerless to get Rodney back, powerless to help the men and women lying in the infirmary. She had stood on the balcony as the body bags containing the three marines who had died in the explosion and the sparse remains of Doctor Benedict were carried to the mortuary; they would join the recovered bodies of Ripley and his team. When she had asked the Irithians about the possibility of Colonel Sheppard and Sergeant McCormack's bodies being returned to them, they had told her that executed prisoners were incinerated.

ooOoo

The narrow iron staircase spiraled up into the blackness. Rodney had no real idea of how deep underground they were but, as best he could see, it was a climb of at least 100 feet, maybe more. He looked at the man at his side. Sheppard had dropped his head and closed his eyes; Rodney felt as much as heard the pilot's heavy sigh.

"I can't do it, McKay." Sheppard swallowed back and his voice faltered. "I'm so tired. I just…I can't." At that moment the Colonel's legs gave way and he crumpled, nearly dragging McKay down with him. Somehow Rodney managed to keep his balance and lowered his friend to the floor. Sheppard breathed in heavily, almost as if he were gasping for air, and a small cry of pain escaped him.

"But we're nearly there. We just…" Rodney looked up at the seemingly never-ending staircase. "Maybe if we rest a little while?" Sheppard's head lolled to one side.

"No. You go."

"No, no you don't. I'm not leaving you." Sheppard forced his eyes open and, reaching up his good hand, patted the side of Rodney's face weakly.

"If they come one of us needs to be up there."

"Okay. But I'm coming back. I'll give the Daedalus a little while but if they're not there I'll come back for you. Okay? Maybe after a rest you'll be able to make it." An instant of eye contact was all it took for Rodney to know that Sheppard wasn't going to be getting out of here on his own two legs. The pilot pushed his flashlight the one they had been preserving, into McKay's hands. He balked. "No, you need this more than me."

"I'm just gonna be sitting here. You're climbing…need to be careful." He pushed the flashlight at Rodney again and this time he took it, reluctantly swapping it for the nearly dead one. "S'okay." Sheppard reassured.

"I'll be back soon."

ooOoo

Halfway up the winding stairs McKay stopped for a rest, hanging on to the rail for dear life. His legs felt like lead and even this flashlight was growing dimmer by the minute, though he had to admit that was probably a good thing because it meant that he couldn't see how far up he was; heights weren't really his thing though, thinking about it, none of this was his thing. Somewhere far below him Sheppard sat in the dark, alone; McKay was reminded of something the Colonel had said, about how the Irithians had left him alone like that for weeks, and that was enough to spur Rodney on, forcing his legs to keep moving.

Eventually he reached the top level and there, built into the sloping ceiling, was a large metal hatch. Collapsing against it, he pushed all of his weight into turning the lock and was surprised when it opened more easily that the other one had. Putting his shoulder against it, he pushed and slowly it opened, tearing plants and dirt from the ground where the local flora had hidden the door from the outside world. Fresh air streamed through the open hatch, the smell of earth and water. Tentatively he poked his head out, encouraged by the fact that no one had stuck a gun through the opening yet.

The lake he had seen from the jumper glistened in front of him, looking around he found himself situated on the gently rolling slopes at the base of the mountain which lay half in shade, half in bright, cool sunshine. The exit was concealed at the edge of a small crop of trees, tangled weeds with delicate blue flowers laced across the top of the hatch. It was beautiful. Even if he hadn't have spent several hours in pitch blackness it would have been beautiful and he found himself reminded of Switzerland; it was a comforting thought.

Based on what he'd seen on the way in, the lake was some distance from the gate which was good. Pushing himself up and fully out, he lowered the hatch back down gently and re-covered it with the weeds that he'd disturbed before sneaking out of the copse. There wasn't any sign of any buildings or activity near the lake and he hoped everyone would be busy, what with the city being invaded and things.

Digging into his pocket, he retrieved the radio Iestyn had recovered for him, turning it on and receiving only screeching static in reply; something in the mountain was interfering with the signal. He had to move further away from it. With a glance back at the hatch and a pang at the thought of leaving Sheppard alone for any longer than necessary, he set off down the slope, heading around the lake and toward the valley beyond.

ooOoo

A little while ago John thought he had heard the hatch up above him open and a rush of cool air against his face but perhaps he had just imagined it. Wishful thinking. It felt like his head was splitting open, the pain like ice-cold knives, but this time he was going to fight it all the way. The darkness was closing in on him, but he wouldn't let it win. He wasn't going to die alone in the dark, not now.

ooOoo

It was getting dark; the sun was moving behind another distant mountain range, a pink tinge around its edges, and as the sky darkened a second planet shone in the sky, bright enough to cast shadows. Once again he tried the radio and this time he wasn't met with static; he felt a jolt of excitement in his stomach.

"Daedalus, this is McKay." He waited a second but there was no reply. "I repeat, this is McKay." Nothing. He sat on the ground trying to quell his panic. "Daedalus, please come in." He put his head in his hands. This could not be happening. He'd walked nearly the whole length of the massive lake and now he'd never make it back to Sheppard before sunset, and even if he did the torch would die long before he got back down the staircase. Distant gunshots erupted, making him start. The sounds were faint but whatever was happening down by the gate, it sounded like a pretty vicious firefight. Maybe that meant the Irithians were winning, they were taking back the gate; if that was the case maybe he could find Iestyn. If he could find the commander he would help them escape, send them back through the gate. He wanted to scream in frustration. How many times did he have to say it, this wasn't his thing, he didn't do heroic.

The radio crackled into life in his hand and he nearly dropped it in his surprise. The voice was slightly garbled, cutting in and out.

"McK…c……is…Tey… McKay…co…in." Jumping up, he put the radio to his mouth.

"McKay to Teyla, can you hear me?"

"Rodney…whe…you." The relief her voice was tangible even through the mangled radio.

"Um…I'm…uh…okay um, where the hell am I? Where are you?"

"Near…st…gate. Where… you?"

His eyes focused on the lake. "Okay, can you see the big lake?"

"Yes."

"Good, um…there's a…" _What the hell was that called? _"…um, a thin pointy bit of lake that kind of sticks out toward the gate."

"Wha…"

"I said A THIN POINTY BIT!" He was already on his feet heading back toward the lake, he just had to make it there before dark. "Look, just move toward the lake."

ooOoo

It seemed like hours before he reached the edge of the lake though he'd have to guess it was in reality little more than twenty minutes. He headed down the shore line towards the arm of water that stretched out towards the gate. In the increasingly gloomy light he found himself stumbling on the rocky ground and the lapping waters of the lake that had looked so beautiful earlier took on a sinister air. The radio had packed up several minutes ago but he was confident that Teyla was heading for the same destination as he was. Lactic acid burned in his legs and his lungs seemed to resent every breath he took, but they were so close to home now, he wasn't going to give up.

It was hardly a surprise as he stumbled toward the rendezvous point to find Teyla, Ronon and Frischmann already there; even in the murky blue light Ronon's looming figure was unmistakable. Teyla rushed forward to meet him, relief plastered on her face..

"Rodney, it is good to see you. Are you alright?" Out of breath and exhausted, he nodded, unable to speak until he'd caught his breath. Bending over, hands resting on knees, he gulped back air. Feeling a hand resting on his back, he glanced up to see Frischmann standing next to him, a gentle smile on her face.

"You okay?"

He nodded again. "I'm fine…but we have to keep going. I left him…and he's hurt, we have to go…" His legs felt like jelly but he forced them onward.

"Rodney, where are we going?"

"Back under the mountain…he's there in the dark on his own and he's all busted up and I left him and it's really cold down there…oh my God, it's really cold, why didn't I leave him my jacket? How could I be so stupid? Great, now he's gonna freeze to death, as if he didn't have enough problems." He turned back to his companions. "What are you waiting for? C'mon."

"Who is hurt?" Teyla asked. He looked at her in exasperation.

"Sheppard." Ronon caught up with him in a couple of steps and grabbed him by the arm.

"Sheppard's alive?"

"Isn't that what I just said? He's alive and he's hurt and we don't have time to stand around here talking. Now are you guys coming or not?"

By the time they had retraced his steps and found the entrance to the shaft it was completely dark; the neighbouring planet that had shone so brightly earlier could only just be seen over the top of the mountain range and was disappearing quickly. The only light they had were the thin beams from Teyla and Frischmann's P-90's; they had barely found the hatch before Ronon had pulled it open, one handed McKay was rather irritated to notice, and disappeared into the darkness. Teyla shone the torch from her weapon down after him.

"Ronon, wait, you cannot see. It is dangerous."

"Then you'd better hurry up and join me." She turned back to the others.

"You should both stay here. Guard the entrance in case there are any retreating Genii soldiers. We shall be as quick as possible."

"Shouldn't I come too?"

"Rodney, you are exhausted. Rest; we will return as soon as we can." Placing a gentle hand on his shoulder, she smiled at him earnestly before following Ronon down into the pitch black.

ooOoo

Carson had just come out of the operating theatre after five hours of surgery on Corporal Hines. That's when he told her to go get some rest, to sleep if she could, and immediately walked back into the operating room to start on the next patient. On her bedside sat the little bottle of cream coloured pills that Carson had given her to help her sleep; it was so tempting to just go back to her quarters and take one, to go to sleep and wake up when the nightmare was over, but she was stronger than that. She heading back out into the city; she was it's leader and now more than ever she was needed. Maybe she couldn't change anything but she could make her presence felt, she could reassure and support her people.

Most of the civilian contingent were still on the mainland with the Athosians. She had contacted them and told them to stay put for the time being; she wasn't going to risk their safety until every last Irithian was out of Atlantis. Lorne had taken control of the military situation; the Irithians still on Atlantis had been put into holding cells, apart from the two leaders who had been allowed to wait in the conference room. Part of her pitied them, they had been manipulated and lied to, their faith twisted, but at the same time she couldn't bear to have them in her city any longer than necessary and she hoped that the attempt to retake the gate would be not only successful but swift.

The Daedalus should have arrived by now and everything had become a waiting game. Her thoughts drifted to Rodney; she wondered where he was, if he was okay. She wasn't sure if she could bear to lose another friend. The thought of Atlantis without both John and Rodney seemed inconceivable.

When the gate finally activated there was a rush of activity toward the control room. Chuck had suffered minor injuries in the explosion so he had been sent to his quarters and, with the other technicians on the mainland, Zelenka had taken his place at the console. He studied it carefully before turning to Elizabeth.

"It's the IDC we gave the Irithians. We have audio feed." The radio message came out over the speakers so everyone in the room could hear it. Lorne had led the two priests in to the control room and they listened to their officer report in.

"We have retaken the gate, but are in desperate need of reinforcements. Please send the rest of the men through quickly. I repeat, we are in need of reinforcements."

Resting her hand on the back of Zelenka's chair, she replied to the message. "The rest of your people will be joining you as soon as possible." Her relief at the prospect of getting rid of the Irithians must have been plain on her face but she didn't care. "Major, get the rest of them up here and through the gate. Return their weapons one at a time as they go and have them heavily guarded at all times."

"Yes, ma'am."

She turned to the priests. "If you need to contact us again you can use the IDC we gave you. We will not be opening the shield for you anytime soon but I think it is within the best interests for both our people if we stay in contact. I honestly hope that you succeed in repelling the Genii invasion force, and perhaps in time we can learn more about one another's people; however, you have murdered innocent men and women in cold blood, and that is not going to be forgotten in a hurry." They all looked round as the first group of soldiers were led into the gate room surrounded by heavily armed and armoured marines. "Now. Please leave."

They inclined their heads toward her and she returned the gesture. She offered her hand to Glahan and he looked at it curiously.

"It is a custom of my people, to shake hands. It is a traditional way of both sealing an agreement and saying goodbye."

"Of course." He held his hand out slightly warily, she took it and gave it a brief firm shake before offering her hand to Arlais and repeating the action. "I know you may find it hard to believe, Doctor, but we are truly sorry for what has happened here."

"We have a saying, Lord Patriarch 'actions speak louder than words'. Perhaps you should bear that in mind."

He smiled ruefully. "It is a wise saying. Goodbye, Doctor." She watched as the two priests joined their troops leaving through the gate; she couldn't wait for Atlantis to be free of them. They were among the last to go, looking wistfully around the gate room before they did, and when the gate finally closed down she breathed a sigh of relief and walked away.

OoOoo

"…John?" Gentle hands touched his face and through his half open eyes he could see lights dancing in front of him. Abruptly pain wrenched through him as he felt himself lifted up from the ground and pulled into a standing position. He cried out and his eyes opened wide with the shock.

"Sorry, Sheppard but we don't have a lot of choice." A gruff voice close to his ear and strong arms holding him up.

"Ronon?"

"Yeah."

"Teyla?" As his eyes began to focus he made out her soft features, barely visible in the murky light. She moved forward, putting her arm around his waist and taking his weight, and he pulled her closer even though it made him wince at the pain. She seemed to understand the gesture.

"I missed you too, John." she whispered.

"McKay?"

"He awaits us on the surface."

"Atlantis? They're attacking…"

"That has been taken care of. Do not worry yourself, all will be well. Now we must get you out of here."

He'd never felt so weak in his life. "I can't…"

"You won't have to."

Ronon bent down and tossed Sheppard over his shoulder. He screamed in pain, feeling like his chest was being crushed; he wanted to throw up but his stomach was already empty. The Satedan clung on to Sheppard's legs with one hand and started up the stairs, Sheppard lolling over his shoulder, and behind them John could see Teyla start to climb, the light from her P-90 dancing back and forth with her movement. The stairs might as well have been a mountain as far as he was concerned, but Teyla and Ronon made light work of them.

As they reached the top and made their way out of the small hatch, Ronon adjusted his hold on him and he felt something shift in his chest and a thin blade of pain shot through him, then everything seemed numb and peaceful as Ronon laid him gently down on the cool grass. He looked up into a velvet sky filled with a million stars, the crisp mountain air washed over him, taking the pain and exhaustion with it; beautiful didn't come close as a description. The moment was somewhat spoiled by the vision of Rodney McKay's face looming above him.

"Are you okay?" The scientist furrowed his brow. "What are you grinning at? Oh great, he's delirious again." The cough racked through him, bringing the pain back tenfold, and he saw McKay back away, a look of horror on his face as the light from the torch caught the mist of blood that he had choked out into the air. Panic erupted around him as the world melted away into nothing.


	16. Pactum Serva

_A/N:- Remember how I told you there was only going to be 4 more chapters a couple of chapters back...well...um I didn't lie as such I just got a teensy bit carried away. Now I promise there will only be 4 more chapters after this one...honest!_

_Now, isn't about time dear Shep went home? _

* * *

**Chapter 15**

**Pactum Serva**

Rodney could only watch in alarm as the medics swarmed around his stricken friend. Streams of incomprehensible medical jargon were called out as Sheppard's ragged clothes were cut from his body, revealing the true extent of his injuries. Rodney felt the colour drain from his own face as he saw the savage bruising on the Colonel's torso. Looking at the fragile body at the centre of the chaotic medical bay, Rodney found himself incredulous that Sheppard had managed to stay on his feet so long but then again, he thought, the pilot had always been a stubborn son of a bitch.

A sudden thought brought Rodney back to himself and he moved forward, panicked. "They drugged him!" He reached out a hand, pointing at Sheppard. "Lots of drugs!" A nurse broke away from the bed and headed toward him, taking his raised arm and gently leading him to one side.

"Do you know what they gave him?" she asked.

"Of course I don't know what they gave him!" His tone of voice made clear his disbelief that she would ask such a stupid question. "Do you really think I stopped to ask?" He glanced over her shoulder at the team working on Sheppard. "What are they doing? Should they be doing that?"

"We have everything under control, Doctor McKay."

"Under control? Is that woman a qualified doctor?" He pointed an accusing finger at the petite young woman who appeared to be issuing the orders.

"Yes, of course."

"Only she really doesn't look old enough to be fully qualified."

"Well I assure you she is. Doctor Jacobs is one of the best. Now if you'd just…"

"She can barely be out of high school, for God's sake!" he interrupted. He felt a gentle tug on his hand as he watched the nurse turn away and head back to Sheppard. He snapped his head around to see Teyla, a worried expression etched on her normally serene features; her dark eyes flitted between Rodney and Sheppard.

"Let them look after John and let a nurse look at you. Some of your bruising looks painful."

"Painful?" He looked at her like she was insane. "Look at him!" He pointed at Sheppard. "That's painful! This is nothing. Where the hell is Carson when you need him? He should be here."

"Rodney, calm down, you are making your lip bleed." He could feel the warm bubble of blood building on his swollen bottom lip and wiped it away with the back of his hand. As he looked down at the blood streaked across his hand, he noticed he was shaking. Once he'd noticed the tremor it seemed to grow until his whole body shook uncontrollably and his heart thumped wildly in his chest as he gasped for breath in short shallow gasps. Looking at Teyla, panic overtaking him, he opened his eyes wide, silently begging for help. Wrapping an arm around him, she gently led him toward a bed, all the while talking in her soothing voice but all the words jumbled into each other and it became just an indistinct murmur. The room started spinning wildly and the last thing he saw was Ronon moving forward to catch him as he fell.

ooOoo

Carson had made her promise to get some rest. She'd made him promise the same; the care worn into his face had aged him in a matter of hours, his normally gentle blue eyes grown tired and hard. He'd seen too much death, they all had. Five soldiers had died in the initial explosion, they'd lost one more on the operating table. Austin was still critical, as was another marine, and a third was stable but had lost a leg. Then there were assorted minor injuries, most of which had been returned to their own quarters to save space in the already packed infirmary.

She felt guilty at taking the time to return to her own quarters but she felt the need to be clean. She stood in the shower and scrubbed away the dirt that still covered her from the explosion in the gate room. She found marks on her arms where she had been hit by tiny pieces of shrapnel and, stepping out of the shower, she wiped the condensation from the mirror to see the same tiredness she had seen in Carson on her own face.

It hadn't been her intention to fall asleep, she had only lain down for a moment, but somewhere along the line exhaustion had got the better of her and she had drifted off to sleep. She awoke with a start as her earpiece activated and she heard Carson's quiet voice in her ear.

"Elizabeth, did I wake you love?"

"Um…that's okay." Glancing over at her alarm clock, she was horrified to see four hours had passed. "Carson, has the Daedalus made contact yet?"

"Yes, actually that's why I'm contacting you." She got to her feet, trying to shake off the groggy feeling of sleep. She was still pulling on her boots as she made her way to the door, a delicate balancing act that almost landed her in a heap in the corridor.

"Rodney?"

"And Colonel Sheppard." The breath was knocked out of her at his words and she stopped dead in her tracks.

"What? Alive?"

"It would appear so." She was back running, heading for the transporter. "They're still three hours out but Doctor Galloway is sending me details of their medical conditions now."

"I'm on my way." Diving into the transporter, she hit the button, stepping out and breaking in to a jog. Entering the crowded infirmary, she spotted the Scot bending over a laptop as information scrolled down the screen.

"Carson?"

"Good news is Rodney doesn't appear to have any serious injuries. "

"And John?" Despite her best efforts, she couldn't hide the mixture of hope and panic in her voice.

"Not so good." Carson rubbed his face wearily as he studied the screen. "Bloody hell! It'd be easier to list what injuries he doesn't have."

"But he's going to be okay?" Carson stood up straight. When he looked at Elizabeth it was with his patented Doctor's expression.

"The medical crew on the Daedalus are excellent and are doing everything they can."

"That's not answering my question, Carson."

"I'm sorry, Elizabeth, I can't give you an answer. I'll have a better idea when they get here."

ooOoo

Elizabeth spent the next two and a half hours wandering the halls of Atlantis. Now that the Irithians were out of the city, a shocked quietness had settled. She visited the injured, talked to the distressed and welcomed back the civilians from the mainland. A group of Athosians had come with them, offering assistance in anyway they could. Before Elizabeth could decline the offer, they were already setting about cleaning up the debris in the gate room.

With half an hour to go before the Daedalus was due home, she took up residence in Carson's office and watched as he oversaw the preparation of two beds, one in the ward for Rodney and another in the already crowded ICU. Through the glass she could see nurses setting up an array of equipment and monitors around the bed.

The medical staff were exhausted; Carson claimed to have had a couple of hours sleep but still looked fit to drop. She had caught her own reflection in the glass walls around the infirmary and knew she looked equally as bad. Her four hours of sleep had only served to highlight her need for rest; she sat nursing a cup of the strongest coffee she could find, gulping it down as if it were medicine, never really tasting it.

She felt her heart lurch as Colonel Caldwell's voice came over her earpiece announcing their arrival. The increase in tension in the medical staff in the infirmary was visible. Carson lifted his hand to his ear as he spoke to the doctor aboard the Daedalus and then, turning briefly to look at Elizabeth, he let them know he was ready.

A quick flash of white light and Rodney was there, laying on the bed in front of her, looking dazed and exhausted, his face ashen. A nurse and doctor were quickly at his side. Another flash through the glass in the ICU and a second figure appeared on the empty bed. Carson wasted no time in moving to the bedside; the doctor from the ship had beamed down with Sheppard and was already filling the Scotsman in. Elizabeth stepped forward, craning her neck to see through the glass dividing wall, wanting to see; she furrowed her brow, part of her unable to believe that the fragile body lying in the bed was John. She caught another flash of light out of the corner of her eye and felt a hand wrap around her own and squeeze gently. She knew it was Teyla. She turned to the Athosian.

"The doctor says he is stable."

"Was he conscious when you found him?"

"Barely. But he recognised us and was worried about Atlantis." Elizabeth let out a small, breathy sigh.

"That sounds like John. Always worrying about everyone else." He'd been coherent enough to worry about them; that gave her some hope. "And Rodney?"

"He had us worried; he lost consciousness and appeared to be having trouble breathing. His blood sugar levels were dangerously low and he is suffering from exhaustion and shock. But he is more concerned for the Colonel than himself." And if Rodney was more concerned for John than himself then it had to be bad, Elizabeth thought.

She watched as one of the nurses pulled the screen around John's bed. Ronon had seated himself behind them and in the reflection in the glass she could see him, his head resting in his hands, the closest she'd ever seen him come to displaying any emotion beyond anger, though she suspected he was also feeling a great deal of that right now; she knew she was.

Once the chaos of the infirmary had settled down, she broke away from Teyla, offering her a grateful smile, and found her way to Rodney's bedside. The bruises around his neck were developing into deep purple handprints, the left side of his face was also bruised and there was a single black stitch in his cut lip. She didn't think she'd ever seen him look so exhausted or so pale. He sat up on the bed, his eyes fixed firmly on the screens on the other side of the glass, almost as if he could see through them to his friend lying behind. The nurse was attaching a heart monitor to him but he barely seemed to notice.

"Rodney?" She tilted her head in an attempt to make eye contact. "You don't know how relieved I am to see you in one piece."

"I found him. I found him and I brought him home and now the son of a bitch is gonna die on us." She took his hand gently in her own.

"Carson will take good care of him…and he's a fighter." If Elizabeth had to describe John Sheppard, that was one word that would always come to mind. "What happened?"

"Kolya! Kolya did that to him." He spat the name out as though it was a curse. As far as Elizabeth was concerned, it was; that one man had caused so much misery and death.

"And Sergeant McCormack?" A shiver seemed to run through him.

"They shot him, blew his brains out; Sheppard saw it, they made him watch." He wrenched his eyes away from the ICU and turned to look at Elizabeth and she could see the anguish in his eyes, tears barely held back. "He was there alone all this time being tortured and God knows what…" He trailed off for a moment. "He's got to get better, he's the hero. That's how it works right?"

"Yeah, that's how it works."

She tried to smile but, seeing his face so openly scared and vulnerable, Elizabeth failed in her attempt to hold back her own tears. Stepping forward, she wrapped her arms around the scientist, pulling him into a tight hug, and she let the tears fall. Now the dam that had been holding back the emotions had been breached, she found all the pain of recent times coming to the surface; so she cried. Cried for Rodney and for John and for all the people they'd lost.

ooOoo

Despite his exhaustion, Rodney had fought sleep to the last but eventually his body won the fight and he drifted off. Elizabeth sat with him, watching as the lines of stress on his face slowly dissolved away. He looked so peaceful. She couldn't help but feel a little jealous of him; she knew it would be a long time before she'd find peace in sleep again. The infirmary was calm now, just the low sound of breathing and the quiet beeps of the monitors, so when Carson spoke she almost jumped out of her chair.

"I'm sorry, Elizabeth. I didn't mean to startle you,." he said. "I just thought you might like to see him now."

"Is he awake?" she asked, standing up.

"No, love. It's going to be a good few hours before he wakes up. To tell the truth, I'd be happier to see him awake, the head wounds are worrying me a wee bit, but his other injuries and his condition generally complicate matters." Elizabeth followed Carson through to the intensive care unit. The screens were still pulled across and when she stepped behind them she felt her breath catch in her throat; it really was John, just not the same John she had last seen on a sunny day what seemed like a lifetime ago.

As she had been when he had first been transported down from the Daedalus, she was struck again by how fragile he looked. His face was gaunt, a fact only exaggerated by the close-cropped hair. An ugly scar ran from his hairline back toward his crown. On the same side his eye had swollen completely shut and bruising mottled seemingly every inch of exposed skin. His wrists were bandaged and one hand was arranged in a complicated splint. As well as the array of monitors, two chest drains ran out from under his gown.

"He suffered severe pulmonary contusions, bleeding both into the lung itself and into the chest cavity."

"But he's breathing on his own?" she asked, surprised.

"Aye. Which is a good sign. Chest injuries will normally heal themselves, we'll just use pain management to keep him comfortable and let nature take its course."

"And he will recover?"

"Normally, I'd not hesitate to say yes. But normally the Colonel is in excellent physical condition. As it is, he's malnourished and has a whole host of other injuries." Carson sighed heavily. "But even so, I'd like to think the odds are in his favour. The next few hours are the important ones." Elizabeth reached out and laid her fingers on the sheet beside John's arm, scared to touch him.

"What happened to his hand?"

"The bastards broke his fingers. Not the most original torture method but a damned effective one, I'd wager." She could see Carson's mouth twist in disgust and it suddenly brought it home to her, the fact that John had been held prisoner by these animals for so long, and she felt sick at the thought. She remembered back to Rodney's words, what he had said about McCormack's death, and looked at the man lying sleeping on the bed, his skin so pale it almost matched the white sheets, and realised that healing John Sheppard's body was only half the battle.

"You should get some more rest."

She forced a smile. "Look who's talking."

"Aye and you're right. I'll get some sleep if you do." They both looked at the sleeping figure. "He'll be well taken care of. And he'll get through this, I know he will. We've just got to have a little faith."


	17. The Cold Light Of Day

_A/N: Thank you all as always for the feedback and for sticking with me. And just because I haven't said it in a while, thank you to my fabulous beta Alipeeps without whom this story would be unreadable. _

* * *

**Chapter 16**

**The Cold Light Of Day**

_He loved the sound; it was a like a heartbeat, the machine was part of him and he was part of the machine. There was no other rush like this, watching the ground scroll away beneath him, feeling part of the clear blue air, reaching up and touching the clouds. Sensations flooded his mind, colours and tastes. Afterwards he had sat in the cockpit not wanting it to end, not moving until he felt a hand on top of his head ruffling his hair. Turning, he saw his father grinning at him._

"_C'mon buddy, time to go." His Dad leant forward and plucked him from his seat and carried him back across the airfield. He looked back at the helicopter longingly. "Hey, cheer up! I'll take you up again next weekend, if you want." He nodded vigorously and was rewarded by another grin from his father. "Well alright then, I guess that's what we'll do, John…"_

"…John? John, can you hear me?" His eyes flickered open briefly, or at least one of them did; it closed again quickly at the stinging bright light. His father's voice had taken on a distinctly Scottish burr.

"The light's gone now. C'mon son, open your eyes for me." He finally put a name to the persistent voice and, forcing his eye open once more, a blurry vision of the man himself appeared in front of him. Beckett. "That's it."

"Sleeping," he mumbled.

"I know and I wish I could let you. Do you know where you are, son?"

His vision flickered across the ceiling and then back to the doctor.

"Home?" That elicited a smile from the Scot.

"Aye, son. You're home. And we're all very happy to have you back, I can tell you."

The pressure on his face, he realised, was an oxygen mask. He tried to shift his position on the bed but found his body unresponsive. He looked up at the doctor, a flutter of panic in his stomach.

"Numb."

"Don't worry, that's the analgesic. That's so you can breathe normally without any pain. We've put an epidural catheter in; we're going to have to keep you like this for a while I'm afraid." John relaxed; Carson was the only doctor he'd ever had complete faith in. If the Scot said he was going to be okay, he believed him. He felt his mind drifting again and battled to keep his eye lids open. "It's alright, lad," Carson said upon seeing his struggles. "Just a couple of little checks and you can go back to sleep."

OoOoo

Rodney slipped out of his bed, wincing as his bare feet touched the cold floor. He knew that Sheppard had briefly woken up earlier and Rodney had told Beckett exactly what he thought of not being informed of this development so, upon hearing the doctor's soft voice coming from the vicinity of Sheppard's bed in the adjoining room, he decided to go and investigate. Tiptoeing the short distance to the ICU across the tiled floor, so as to avoid the wrath of the nurses, he pushed his way through the curtain and, ignoring Beckett's protestations, leaned over the bed, peering at Sheppard's face.

"Is he awake?" Rodney asked the doctor before addressing the patient directly. "Are you awake?"

"No. Go away," came the mumbled reply. The scientist narrowed his eyes.

"And here was me hoping that a crack on the head might actually have improved your personality."

"Least I have one." The reply came back without hesitation and some of the tension in Rodney's face washed away and was replaced by a glint of amusement; this was more like how things should be, a constant game of one-upmanship.

"Well, I see you're back to your old self. I told Carson you'd be fine." He pretended not to notice the doctor rolling his eyes. "So, are you going to thank me for saving your skinny ass or what?"

Sheppard smiled, at least Rodney thought it was a smile; the Colonel was already slipping into unconsciousness again as he mumbled, "I knew you wouldn't leave me behind…" Rodney opened his mouth and then shut it again, before sitting down heavily on the bedside chair and watching his friend drift back to sleep.

ooOoo

It was 6:30 am. It had been two days and the city had settled into a kind of shell-shocked stillness. The infirmary was quieter now, a world away from the frenetic environment of the last two days. Each bed was full, as were those in the adjoining room. Elizabeth's gaze was drawn to the curtained-off bed just inside the door of the ICU. Rodney had somehow persuaded Carson to let him have the bed at the end of the ward so he could keep an eye on John through the glass.

"Good morning, Rodney."

"Ah! Elizabeth." He smiled, wincing as the stitch in his bottom lip pulled.

"You look much better this morning."

"Well, I guess I don't look too bad for someone who's been through a hideous ordeal." He poked gingerly at his lip until Carson walked up and swatted his hand away.

"Hideous ordeal? Sounds rather like having you for a patient." The physicist sneered at Carson. "And your lip wouldn't hurt so much if you'd keep quiet for five minutes."

"It wouldn't hurt so much if you gave me strong enough painkillers."

"Rodney, you don't need painkillers," the medic sighed.

"Easy for you to say, you're not the one in agony." Rodney croaked out his words, rubbing his bruised throat as if to prove a point. Elizabeth shook her head at him and turned to the physician, who looked pale and drained.

"Carson, you need sleep." He cast her a sideways glance.

"Hark who's talking. You know as well as I do, Elizabeth, we don't have the medical staff to deal with this many patients. We've worked out a rota system but none of us are going to be getting much sleep for the next few days." He picked up McKay's chart and scribbled a note on the bottom of it. "At least we'll be shot of this one later today."

"Hey! I'll have you know I'm the model patient, the fault lies with the doctor."

"Rodney!" Elizabeth scolded, raising her eyebrows; he sank a little lower in the bed. "So Carson, can you give me something to smile about this morning?"

"Well, the news is bittersweet, I'm afraid. Sergeant Hunter has improved overnight, he's still critical but stable and his progress is as much as we can hope for. Corporal Warren has lost her leg, as you know, but she's doing really well; I'm confident she'll make a good recovery."

"That's something."

"Unfortunately, Corporal Austin isn't doing so well. He's not responding to treatment; we're doing all we can but quite frankly it doesn't look good, the damage is too extensive." Elizabeth folded her arms across her chest, wondering when the nightmare was going to end. Her eyes drifted to the curtained-off bed through the glass.

"And John?"

"It was a close run thing but Ronon and Teyla got him here in time."

This time Rodney looked genuinely wounded. "Ronan and Teyla? I was the one who did the brave rescuing bit, they just turned up at the end."

Elizabeth smiled at him. "We know that Rodney, and I for one am extremely proud of you. Especially bearing in mind your own injuries." An expression of contentment took up residence on his face, a typical Rodney reaction to flattery, she thought to herself, but in this case what she'd said was true - the scientist had acted with strength and courage. Rodney had changed a great deal in the past three years, friendship tended to do that to people and, whether they'd admit it or not, somewhere along the way Rodney and John's friendship had become pretty much unbreakable. She turned her gaze back to the curtained-off bed and spoke to Carson. "He's going to be okay?"

"I think so. He's doing well. His chest injuries are going to be a long while healing and the head wounds are a little bit of a worry, there's two separate skull fractures. It's going to be a long and painful road for him but the fact that he's still with us is testament to how tough he is.

His hand is a bloody mess, quite frankly, and it'll never be as strong as it was but with physiotherapy it shouldn't hinder him. Most of the other bruising is…superficial, for want of a better word. He's lost a lot of weight, as you saw, and there's some muscle atrophy, not to mention that they were pumping him full of enough drugs to knock out an elephant." Carson's eyes stared at the curtain, almost as if he could see through it, and his voice sounded distant. "He's a tough little bugger that one."

"Yes, he is. Has he been awake?"

"Aye. We're having to wake him up every couple of hours, just briefly, but he knows where he is and how he got here. Even had the presence of mind to insult Rodney."

That made Elizabeth's smile widen.

"That's all the thanks I get for saving his life," the scientist grumbled.

"May I sit with him for a while?" she asked. Carson nodded and patted her arm.

"Go ahead."

Stepping through the glass door and slipping inside the curtains, she sat down in the chair beside John's bed. Behind her, she heard Carson bullying Rodney into taking a shower, assuring the Canadian he didn't need a wheelchair to make it to the bathroom. John lay with his head slightly to one side; his skin was so pale it was nearly the colour of the white sheets, which made the ugly bruising even more difficult to look at, and the black stitching of the cut running from his hairline back toward his crown made her wince just to look at it. At least the swelling around his eye had lessened a little.

Noticing that his oxygen mask had slipped, she leaned forward and tried to readjust it, snatching her hands away as he suddenly moved and his eyes opened. He looked up at her, momentarily confused, and after a second she saw his face relax.

"Hey," he drawled.

"Did I hurt you?"

"No. S'fine." His eyes drooped shut and for moment she thought he had fallen back asleep but they opened again drowsily. "Brain feels like mush."

"Nothing new there then." The corner of his mouth twitched upward into something resembling a smirk.

"Did I ever tell you your bedside manner sucks?" Although the words were slurred with sleep and his eyes were hazy, she couldn't help but feel relief at this little piece of normalcy.

"Several times."

His dark eyes focused on her, his brow furrowing slightly. "You okay?"

Letting out an astonished laugh she shook her head. "Am I okay? John, look at you."

"Answer the question, Doctor."

"I'm just…It's been a hellish couple of days - couple of months."

"How many have we lost?"

"Twelve."

"Twelve," he repeated, his voice barely audible. "Could've been worse."

Elizabeth nodded, feeling a knot in her stomach. "I know. We have three more in intensive care." She looked around at the assorted machinery. "Four if we include you."

"I'll live." He frowned at her. "I am gonna live, right?"

"Yes. It looks like we're stuck with you."

"Sorry 'bout that!" She gently gripped his arm and swallowed back the lump rising in her throat.

"I'm not."

ooOoo

The next time John woke, it was to the sound of voices shouting instructions as Corporal Austin was rushed back into surgery. They never brought the young man back into the infirmary. Questioning one of the nurses the next morning, he found out that the young marine had died on the table.

Elizabeth checked in on him first thing, making sure he really was still there, before visiting all the other wounded and being briefed on their conditions. He wondered if she had slept at all since he last saw her and came to the conclusion that she probably hadn't. Teyla sat with him most of the morning and, after some badgering and in-between his frequent dozes, told him about what had happened over the last few weeks, filling him in on the details of the invasion and the events leading up to it, though he suspected he was getting a sanitised version. Not long after she left, McKay came and sat with him until Carson kicked him out of the infirmary and sent him to rest in his own quarters. Ronon stayed clear but he had expected as much; the big man wasn't one for words and he avoided the infirmary if he could get away with it.

Over the next few days things fell into a routine; Elizabeth would always visit first thing and then do the rounds of the other patients, McKay and Teyla would visit everyday, even if it was only for a short while, and various others popped in from time to time, even Caldwell making friendly but slightly awkward conversation. In between visitors he drifted in and out of sleep but, as his periods of consciousness grew longer and his frustration at being immobile became increasingly manifest, he slowly felt the euphoria of getting home ebb away. So when Kate Heightmeyer turned up at his bedside, he wasn't surprised to see her.

"How are you feeling, Colonel?"

"I've been better." Her smile seemed genuine enough but he'd never really trusted psychologists; you could see their minds working overtime, thinking out every word before they spoke, calculating their expressions and picking up on harmless comments and turning them into "issues".

"Sorry, that was a bit of a silly question, wasn't it? You've been through a very traumatic experience."

"Hasn't everyone? You must be wishing you got paid by the patient right now." He noticed her tense up and felt a little guilty for his harshness. "Sorry. I guess this hasn't exactly been easy on you, there must be a lot of screwed up people out there right now."

She settled herself into the chair next to the bed and rested a notepad on her knee. "Why do you do that? Transfer everything on to other people? From what Carson and Elizabeth tell me, you've been worrying about everyone but yourself. Right now you need to concentrate on you."

"I'll be okay. I've been…"

"Through worse? Really?" Raising her eyebrows she looked at him, incredulous.

"No. Not exactly," he had to concede. "Though nearly mutating into a bug wasn't exactly my idea of a good time. But at the end of the day you pick yourself up and you carry on."

"Sometimes that's easier said than done. I know you've been through some tough times before, and you've always coped remarkably well, but we all need a little help now and then."

"I really don't see that talking about it is going to do any good. It's not going to change anything, it won't bring those thirteen men and women back from the dead."

"You think you're responsible for their deaths?"

"And there you go twisting my words. Chances are, if I'd been here people would still have died, you don't have to tell me that, but I was their CO and that alone makes me responsible for them." He tried to think of a way to explain it. "It's like being a parent; their lives are entrusted to you and you do everything in your power to keep them safe."

"By sending them into a war zone with big guns?" She raised an eyebrow.

"It was an analogy. You know what I meant."

"You couldn't have prevented what happened here, you were captured."

"I was careless." She leant back in her chair and he gritted his teeth as he watched her scribbling down notes. "I'm tired."

"Well, that's a not too subtle way of telling me to go away."

"We're in the middle of a crowded infirmary. Forgive me for not wanting to bare my soul to you."

"Would you be anymore inclined to talk to me if we were in my office?" His silence must have given her the answer to her question. "No, I thought not." Standing, she nodded briskly. "Okay. I'll leave you alone for now but remember, even when you're physically fit, you're not going to be cleared for duty until I say so."


	18. Pain On Pain

_A/N_ :- _A really quick update this time. I'm in two minds about this chapter, there are things a I love about it and things I hate, it's a case of me having some decent ideas but not the skill to write them as well as I would have liked. So sorry about that!_

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**Chapter 17**

**Pain On Pain**

Rodney had brought him pastry. John looked at the plate in front of him and cleared his throat in an effort to hold back the grin that was threatening to appear on his face. Sometimes McKay offered up the opportunity to tease him on a plate and this time he'd done so literally. John raised his eyebrows slightly and turned to his companion, keeping a serious expression.

"Rodney, are you trying to tell me something?" The scientist looked back at him blankly. "It's real nice of you to bring me pastry, and I'm flattered and everything, but I just don't feel that way about you." He couldn't help breaking into a smirk, especially at the expression on McKay's face when the penny finally dropped and he remembered the conversation they'd had about Frischmann back under the Irithian city two weeks before.

"Ha! Ha! Very funny, rather like your hair in that photograph Elizabeth has."

"What photograph?" John asked, both perplexed and curious.

Rodney's trademark smug smile glowed even brighter. "You'll have to ask her about that. So, how long before Beckett releases you?"

"He hasn't said yet but I'm walking on my own, well kind of, and if I'm a good boy he's going to let me take a shower all by myself later. Now what's this about a photo…" At that moment McKay's eyes snapped up at the sound of a voice talking to Carson and John turned around and took in the blonde soldier. "So that's her, huh?"

"Yep!" McKay waved his hand in the air and John couldn't help but smile at the slight flush in the scientist's cheeks. "Izzy! Come and meet Colonel Sheppard." She walked over, smiling politely, and Sheppard had to admit that McKay had good taste. Reaching the bedside, she saluted crisply.

"Glad to finally meet you, sir. Well, we kinda already met but this time you're conscious."

"That's always useful when making new acquaintances, I find. So, you haven't shot Rodney yet, I'm impressed." McKay sneered at him while the captain chuckled.

"I find as long as you keep his sugar and caffeine levels up, he's fine. Though if you have any advice on how to handle Ronon, I'm all ears."

"Ah, Chewie's not so bad."

"Chewie?" She raised her eyebrows.

"The Colonel is under the delusion that he's Han Solo."

"Rodney's C-3PO," John added with a beaming smile.

She smiled back nervously and glanced at McKay. John knew that a lot of the new recruits to Atlantis found him difficult to judge at first; he wasn't your average commanding officer. After a brief moment she seemed to realise this was normal behaviour for him and relaxed.

"Now you come to mention it, there is a resemblance." Rodney folded his arms in indignation and she positively beamed at him. "Well, I'd better get going. I'll see you later, Rodney. Good to finally meet you, Sir."

"You too." She was barely out of earshot before he turned to McKay. "As much as I hate to admit this, I think she actually _does_ like you."

"Told you so." Rodney answered smugly.

John shook his head "And at first she seemed so normal. I'm going to have to read the psych reports on new recruits a little more closely in future."

"You're a real comedian today, aren't you? So how long roughly before you can come back on active duty?" John looked away and busied himself pulling the pastry apart; he knew active duty was a long way off and he wasn't up to thinking about it just yet.

"Rodney, you're looking at months. I thought you'd be keen to keep Frischmann around a little longer."

"Well, yes, but it wouldn't be very professional of me to ask her out on a date while we're on the same team."

"So you only want me back so you can hit on her?"

"No, not just that. It's not quite the same without you," he admitted. "I just want the old gang back together." _The old gang?_ An image of Aiden Ford flashed through John's mind, one more person he'd let down. "Sheppard? You okay?"

"Yeah, I'm fine."

McKay shifted uncomfortably and leaned toward John. When he spoke, his voice was lower. "You know if you need to talk to someone about…stuff, I'm here." The sentiment was genuine but he could tell by the tone of voice that McKay was hoping he wouldn't take him up on the offer.

"Stuff?"

"You know what I mean, about what happened to you, what they did to you." He looked embarrassed. "We're worried about you."

"We? Been talking about me, huh?"

McKay sighed with frustration and rolled his eyes. "As a matter of fact, yes. I know you think you can cope with this on your own but you can't."

"I never said it wouldn't take a little time."

"I know, and no one's expecting miracles, but…you laugh and smile and try and act like it's all okay but it's not, is it?"

"You've been talking to Heightmeyer."

"Which is more than you've been doing." Irritable was a far more natural state for McKay than sympathetic. "You know she won't sign you fit for duty until you talk to her and, under the circumstances, I don't blame her. Have you told anyone what happened to you while you were held captive?"

"I told you."

"No. No, you didn't."

"Why are you doing this? Why can't you just leave me alone to deal with it in my own way?"

"Because you're not dealing, you're just avoiding."

It was John's turn to roll his eyes. "Now you're starting to sound like her; if you even think about using the word 'closure' I will not be responsible for my actions." The curtain to the left of his bed was drawn back sharply and a visibly irritated Scottish doctor glared at them.

"There are other patients in this infirmary. Keep your bloody voices down."

"Sorry, Doc. Rodney was now leaving." The scientist snorted and stomped out of the room. John tried to ignore the stab of regret at the argument as he watched the scientist leave.

OoOoo

All those weeks alone in his cell and he'd craved just the sound of a human voice but now, after 12 days stuck in the infirmary, a large proportion of those flat on his back unable to move, the prospect of just a few moments in a room on his own had him almost buzzing with excitement. He pushed the feeling back, attempting to radiate his usual nonchalant air, but he suspected he was failing miserably. His feet were twitching, eager to get out of the bed, but he was patient, not wanting to lose this newly-earned privilege. How bad had things got that he was this excited at being allowed to have a shower on his own? Of course, they wouldn't let him lock the door and he'd only get a few minutes but it was something normal and it seemed a lifetime since anything in his life had been normal.

They'd been slowly getting him back on his feet the last few days; the first time he'd stood up, the room had spun wildly and it had been only the nurse and Carson holding him up as his legs turned to jelly beneath him. But slowly he'd been able to take a few steps on his own; it was standing up that was the worst part, mainly due to the pain in his ribs. He'd been having physio, even when he'd had the epidural catheter in, and God was he pleased to see the back of that. The nurses had come and exercised his legs for him to prevent further muscle atrophy. How pathetic had he felt laying there, unable to feel a thing, while nurses moved his legs for him?

As soon as he saw Carson and one of the nurses, a unerringly cheerful guy by the name of Pete, heading his way, he swung his legs slowly over the edge of the bed. He was still in considerable pain with his ribs and his hand was still useless but since when did he let little things like that get in his way?

"I see you're raring to go. Are you sure you're feeling up to this?" For a brief moment he felt a stab of panic, thinking that they'd changed their minds and weren't going to let him do this, but then he saw the twinkle in the Scotsman's eyes and relaxed, even forcing a smile.

"I'm good to go."

"Okay, now slowly does it." They took up positions one either side of him, letting him put his weight on them rather than trying to hold him up. Once on his feet, it took a moment to orientate himself but now he was upright he actually felt fairly steady and was able to let go. "Now remember, if you feel dizzy or need help, don't hesitate to pull the alarm cord, okay? Pete will be waiting outside for you so don't be a bloody martyr. If I have to pick you up off the bathroom floor you'll be back in bed for another week, do you hear me?"

"Yes, Doc."

"I'm serious, Colonel."

"I assure you Doc, so am I." His feet padded across the cold floor to the bathroom and he couldn't hold back the smile as he pushed the door closed behind him. He'd been dressed in a hospital gown and robe so it wouldn't take him much to undress. Carson had been worried that he'd feel claustrophobic in the tight space but there was nothing here in this brightly lit little room, smelling of a strangely calming mixture of soap and pine disinfectant. Stepping forward, he ran the shower, turning around and dropping the robe and gown onto the towel rail. Then he looked up. He'd not seen a mirror since he'd got back, even shaving was something someone else had done for him, and he hadn't seen a mirror the whole time he'd been held captive. Shock wasn't the word; it was like looking at a stranger. Of course, he knew about his weight loss and that the bruising was still fading. He knew about his hair, he'd even joked with Elizabeth about how they'd given him a damn buzz cut and she'd laughed about how it showed off his pointy ears. He knew about the still-angry scar on his scalp. He knew all those things but it hadn't prepared him for the reality of seeing it. If he looked like this now just how bad had he looked when they'd first seen him? He felt an irrational flush of embarrassment at people seeing him like this.

The knock at the door brought him back to himself and he heard the deep, southern accent of Pete the nurse asking him if he was okay.

"Yeah, I'm good. Just give me a few more minutes." Tearing his vision away from the mirror, he stepped under the warm water, tipping his head back and letting it run over his face, but any thought of enjoying such a simple pleasure as being able to wash himself had disappeared. He quickly grabbed the shower gel and finished. Pulling the robe on awkwardly, he called for Pete and, as the nurse helped him dress in fresh scrubs, he made sure to keep his back to the mirror.

ooOoo

Elizabeth had been sitting at his bedside for ten minutes. She knew he was awake, the muscles in his face were just a little bit too tense, his breathing too even, but he showed no signs of opening his eyes or acknowledging her presence. She never knew what she'd find when she came to visit him. His moods had become erratic; sometimes he was cheerful and talkative, other times he was like this, pretending to be asleep to avoid a conversation. She'd have been offended if it wasn't for the fact that she knew he was like this with everyone.

Sighing, she stood up. If he wanted to be left alone then that's what she'd do. She stepped through the curtain and nearly walked into Carson.

"Elizabeth, are you alright, love?"

"I'm fine, just…frustrated. Has he talked to Kate any more?"

"Define talking." Elizabeth rubbed her temples and Carson gently put his hand on her shoulder. "You know how stubborn he can be. We just need to give him time, under the circumstances depression is normal."

"I know but he's become so erratic. One minute he's laughing and joking the next…you know he swore at Teyla yesterday? Teyla, of all people! He's pushing away the people who care about him most. I just want the old John Sheppard back" She folded her arms and glanced back at the bed. "We left him there all that time, Carson. I just can't help but feel we've let him down."

ooOoo

John couldn't quite believe what he was hearing. Elizabeth thought she'd let him down? What a joke. While Atlantis had been going through hell, he'd been sitting in a cell crying for his parents and waiting to die - wanting to die. And then Iestyn had given him hope and McKay had come and he'd fought it, believed that once he was home everything would be okay - but it wasn't. He was reduced to this, laying in a hospital bed, unable to walk around the ward twice without feeling tired. Warren had a lost a leg and was in better shape than him.

Had he really sworn at Teyla? He couldn't remember clearly what he'd said, just that he'd wanted to be left alone; her constant sympathy had become unbearable, just like Elizabeth's. He didn't want sympathy or pity. Elizabeth had said she wanted the old John Sheppard back, well so did he.

ooOoo

Elizabeth looked at the young Genii woman sitting across the conference room table from her. Caldwell sat to the left in-between them and two marines stood guard at the door.

"So, the Irithians were successful in repelling the Genii force?" Elizabeth asked.

"Kolya's force." Sora corrected her. "Not all of the Genii supported his actions."

"We've heard nothing from the Irithian council."

"And I doubt you will. They expelled us with little thanks once the situation had been resolved. They lost many people and have decided that they are better to stay out of the affairs of others. They will retreat back under their mountain and stay there." All three of them turned at the commotion outside the door. Elizabeth was shocked to see John standing outside in scrubs and robe, arguing with the marines. The two soldiers looked from the senior officer to Elizabeth and she nodded reluctantly. John smiled haughtily at the two men before entering the conference room.

"John, what are you doing here? You look exhausted." He didn't so much as glance at Elizabeth, looking instead straight at Sora.

"Kolya?" He leaned forward, resting his one good hand on the table and putting far too much of his weight on it for Elizabeth's liking. She silently signaled for the marines to call for Carson and stood up, walking over to him. "Tell me he's dead." Elizabeth touched his arm gently.

"John, sit down." He didn't shift his gaze from the Genii.

"I need to know." Sora looked away.

"I don't know. I'm sorry."

"What the hell do you mean, you don't know?"

"He escaped the city but was seriously injured. I've heard nothing since." Elizabeth wouldn't have thought it possible but John visibly paled. Pulling out a chair, she guided him into it.

"He's still alive," he whispered.

"We don't know that for sure." Caldwell interjected. "If there's been no news then maybe that's a good sign. How are things on the Genii homeworld?" John stared at the floor, pain etched on his face and when Elizabeth crouched down and reached out for his hand he gripped hers tightly.

"Tense." Sora admitted. "There is still much debate over Ladon's ability to lead. There is talk of some kind of election."

"Well, that's promising," said the older Colonel. John looked up and briefly met Elizabeth's eyes.

"No offence, Sir, but democracy only works if we like the guy they elect. If there's an election, Kolya will come out of the woodwork and when he does he'll come after us again…and again and again…" Elizabeth squeezed his hand.

"We won't let that happen. He's not going to do this to you again."

"It's not about me. It's all of us. He'll never stop until he has Atlantis. I should have killed him when I had the chance."

"But you didn't because you're a good man." John let out a bitter laugh.

"And look where that's got me." He turned his attention back to Sora. "Um…there was a Irithian guard, his name was Iestyn, he…"

"Helped you escape," she finished for him, her voice quiet and her eyes uncertain. "I'm sorry, but the council convicted him of treason for helping you. He was executed." John's stared at her disbelieving. His breathing grew rapid and he gasped for air as panic overtook him. Elizabeth put her hand to her ear, shouting into her comm.

"Where the hell is that med team? Get up here now!"

She could only watch helplessly while John rocked back and forth muttering under his panting breath, an endless stream of "No, no, no…"


	19. Time Doesn't Heal All Wounds

_A/N:- Well, we are very nearly there now this is the penultimate chapter proper. I'm on to the difficult business of writing emotional angst, I hope I've not strayed too far away from the characters voices. As ever feedback is both helpful and greatly appreciated._**  
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**Chapter 18**

**Time Doesn't Heal All Wounds**

Rodney stood in Carson's office and looked out through the glass dividing wall at Sheppard sleeping in the infirmary and then back to Carson, Elizabeth and Kate Heightmeyer, his mouth opening and closing in disbelief.

"You just let him go wandering off on his own?"

Carson gritted his teeth. "I did nothing of the sort. When I came off duty Colonel Sheppard was resting."

"Oh well! He's certainly resting now, you had to sedate him!" the physicist spat out. He couldn't believe that Sheppard could have not only walked out of the infirmary but reached the conference room without one person stopping him. "He can barely walk to the end of the corridor on his own. How the hell did he get all that way without falling over anyway?"

"Sheer bloody stubbornness, knowing the Colonel." Carson muttered. Rodney was about to speak when Elizabeth raised her hand to stop him.

"Does anyone know how he found out Sora was coming here?" She looked to Carson who just shrugged and shook his head; as she moved her gaze to Rodney he suddenly regretted his little outburst and wished he could shrink back into the wall.

"Um…well…I may have mentioned it in passing."

"Good grief man!" Carson threw his hands up in the air and Kate dropped her head in a heavy sigh. Rodney looked to Elizabeth for back up but she just fixed him with one of those stares.

"Rodney, I would have thought you of all people would have the sense to…"

"I thought I was helping," he interjected, hating the way his voice sounded whiny. "I thought if he knew she was coming here it would prove to him it was really all over. That it'd help him move on." He looked at Kate pleadingly. "I didn't know he was going to react like that."

"Well, next time you decide to practice psychology you might want to ask the opinion of someone who actually has a bloody doctorate in it!" Carson berated.

"I honestly thought it would help him. I just want everything back to normal, or whatever passes for normal in this screwed up excuse for a galaxy."

Kate sighed. "Your heart may have been in the right place, Doctor McKay, but I wish you had spoken to me first. However, what's done is done and at least he can't ignore the problem now."

The four of them looked out at the figure sleeping peacefully on the bed and Rodney felt his heart sink. Sheppard was not going to be happy when he woke up.

ooOoo

Heightmeyer's office was light and airy, the colours soft and relaxing, the furniture arranged to give an informal air. John wondered if this careful design ever fooled anyone; it was supposed to be relaxing but it was too staged and it only served to make it more uncomfortable. It reminded him of the office of the principal at one of his many high schools, one of the few that had been off-base. The principal was heavily into the idea of progressive teaching and wanted to 'relate to students on their own level'. Being called to his office was torture and he doubted this session with Atlantis's resident shrink would be any more enjoyable.

He sat staring out the window, another reminder of his school days, he thought to himself. Kate settled into the chair opposite him, crossing her legs and balancing a file, his file, on her knee.

"How are you feeling today?" He didn't turn to look at her, keeping his gaze on the distant horizon.

"Tired. Just between you and me I think someone drugged me."

"You didn't give us a lot of choice, you were very upset." _Upset._ He knew that didn't even come close. He'd lost it.

"I freaked out in front of half the city. Upset doesn't really cover it."

"Does it bother you that people saw what happened? Do you think it makes you weak?"

"I know it does."

"People don't think any the less of you."

"Of course they do. I'm supposed to lead them, keep calm under pressure, make the right decisions. If I can't do that then I'm not fit to be here."

"You've been through an horrendous ordeal; you can't expect to recover from that overnight. Then on top of that you'd found out the man who did this to you is potentially still alive and your friend had lost his life. Under the circumstances, I think anyone would be entitled to 'freak out' a little bit."

"He wasn't my friend; he was my torturer." Out of the corner of her eye he saw her sit up a little straighter and heard the rustle of paper as she leafed through her notes.

"Iestyn? He was the one who tortured you? You haven't mentioned that before."

"Didn't I?" For the first time he looked at her.

"No. In your report you just said he was commander of the guards."

"Oh." He thought for a minute; his report had been brief and to the point and no one had asked for more. Now he was getting better, he'd be expected to make a full and detailed report, put it all down in black and white, irrevocable proof that it really happened and wasn't just a nightmare. "Well, now you know."

"So why did he help you?" It was a good question; one he'd asked himself, one he'd asked Iestyn. The man had just smiled wearily at him and said 'Because it is right'. John closed his eyes and only re-opened them once he'd turned his head away.

"Because he was a good man in a screwed up world and he tried to do what was right and now he's dead - because of me."

"John, you are not to blame for anything that has happened here. You're as much a victim in all of this as anyone else - maybe more so." She leaned forward, her fingers knitted together, and looked at him earnestly. "And that's part the problem isn't it? You can't cope with the fact that you're a victim."

He couldn't disguise the slight twitch of his facial muscles at the word. Victim. It wasn't a word he associated with himself. He opened his mouth to speak but no words came out.

"You are suffering from post traumatic stress syndrome. You've been in the military for a long time, John. You've seen it happen to others. Have you thought any the less of them for it?" She paused, waiting for a reply, but when she didn't get one she continued. "You have a lot of people who care about you, who thought they'd lost you for good. They're not pitying you and the only one judging you is you."

"I screwed up. I was needed here."

"You were captured."

"By a kid!" He turned to her, his voice laden with self-loathing. "When I was needed, when people were dying here, I was sitting in a cell crying for my parents…so don't tell me I'm not weak because you don't know what you're talking about." Feeling dampness on his cheek, he wiped away the tears with his sleeve and stood up shakily "We're done here."

ooOoo

Carson called this the 'convalescence balcony'. It was a wide-open veranda that sat just off the infirmary. John sat on one of the many benches looking out over the sea and the Daedalus docked beneath him, thinking back over his conversation with Heightmeyer. She'd got what she wanted; he'd lost control and said things he hadn't intended telling anyone, she'd probably call that progress. When had he lost the ability to keep his cool? 'If you were any more laid back, you'd be comatose' Isn't that what McKay always said?

"Do you mind if I join you?" He looked up at Elizabeth; in the bright sunlight all he could see was her silhouette.

"Sure." He waited for her to ask how he was but she didn't, she just sat beside him quietly for a moment before holding something out to him.

"I've been meaning to give you this for a while but I wasn't sure how you'd react so…I never really found the right time." Reaching out, he took the photograph, slightly perplexed at first before registering the young man in the picture as himself. His breath caught in his throat and he felt a flush of colour in his cheeks. Elizabeth tried and failed to suppress a giggle.

"John Sheppard, are you blushing?"

"No," he lied. Then his brain made the connection. "Oh God! McKay said something about a photograph, please tell me he hasn't seen this?" Elizabeth bit her lip and raised her eyebrows in an attempt to look apologetic.

"Sorry!"

"Elizabeth!" he groaned. "Did you show it to anybody else?" She chewed her lip a little more.

"Just Carson and Teyla…and Ronon." At that point she completely failed to hold back her laughter.

"I'm sorry." She swallowed back trying to control it. "But you don't have to look so mortified. I think you look cute."

"Cute? I can think of a lot of words to describe it and that isn't one of them." He sighed. "Where the hell did you get this from anyway?"

"Your father." John turned to her, shocked. "Turn it over." The brief note was scrawled in his father's once familiar hand. A hundred different questions came to mind but he was unable to vocalise any of them so he simply turned back to Elizabeth with a confused expression. "I went to see him, to tell him you were MIA in person."

"And…and you survived?" he stuttered, still bewildered.

"I gave as good as I got." That made him smile; he rather liked the idea of Elizabeth giving his father hell but then, how did she come to have this photograph? As if reading his mind, she continued. "My visit didn't go particularly well but a few days later that arrived for me via Washington. So what do you think? An olive branch maybe?"

"I don't know. I haven't spoken to him in so long. I've thought about him a lot lately; dreamed about him, about how it was before, when I was just a kid and he still…" He paused, choking on his words and when Elizabeth gripped his hand he didn't pull away. "Um…you know how when you're a kid you think your Dad is the coolest man on the planet? Like every superhero rolled into one? I wanted to be just like him - and then Mom died and it was like he didn't know what to do with me so he just kept pushing me away. I tried so hard to make him proud of me but I couldn't be the person he wanted me to be." He sniffed back tears. "Christ, I'm such a wreck. I'm sorry."

"No need to be. You're not the only one with parental issues, trust me. Sometime I'm going to force you to be my shoulder to cry on while I tell you all about my Dad's utter disappointment in me."

"I can't imagine anyone being disappointed to have a daughter like you." Elizabeth smiled.

"Well, I can't imagine anyone being disappointed to have a son like you." She laughed wryly. "Funny isn't it? Even at our age, all we want is our parents to be proud of us." John looked down at the photograph, studying it carefully. "Perhaps you could write to him."

"Yeah, maybe." He cleared his throat. "So, are you going to report this back to the good doctors?"

"Not if you don't want me to but they're only trying to help, John. We all are." Looking back to the horizon, he squeezed her hand gently.

"I know."

He stayed sitting out on the balcony, surprised he hadn't been dragged back to bed; a nurse had come out to administer his meds but then left him to it. A pale sky and dark ocean both ran out toward a hazy horizon and a million different shades of blue played out in front of him. The photograph felt heavy in his hand; the corners were creased where he had toyed with it. The sound of boots on the tiled floor and a shadow cast against the railings signalled company. Sitting down beside him, the figure didn't speak, just joined him in looking out to sea. They sat in companionable silence for a while before he turned to look at the Satedan.

"So, is it your turn to baby-sit me?"

"They're having a meeting about you. I'm supposed to keep you out of the way."

"Honesty. That makes a nice change."

"I figured you'd work it out anyway." They returned to sitting in silence again for a few moments before Ronon spoke. "I'm sorry."

"What for?" The big man looked a little embarrassed as he gestured toward John's chest.

"Your ribs. When I carried you…I should have been more careful."

"You got me out of there, you big doofus. I'd have died under that mountain if it weren't for you."

"Do you wish you had?" The question knocked the air out of John.

"I'm not suicidal. Is that what they think?" He asked alarmed.

"No. That's not what I meant." Ronan turned to face him straight on. "When I was running there were times when…when I just wanted it all to end. I wanted them to just kill me and get it over with but I kept going because I could fight, I was going to take down as many Wraith as I possibly could."

"Is there a moral to this little tale?" John asked sarcastically. He'd never expected this from Ronon.

"Yes, there is. We're warriors you and I; take away our ability to fight and you take away who we are. So maybe that's what they tried to do to you and maybe you wanted to give up - but you didn't. So don't stop fighting now. If you give up, Kolya's won." Ronon stood up. "Besides, no offence to Caldwell but I'd rather have you giving the orders around here." After slapping a hand on John's back nearly hard enough to knock the wind out of him, Ronon left him alone, sitting staring out to sea feeling slightly bewildered at their conversation.

He didn't know how much time had passed before movement below caught his eye but the sun had sunk further in the sky and his body felt tired and heavy and he knew the time for his next set of meds was approaching by the dull ache building in his chest and hand.

He stood up, leaning forward over the railing to get a better view. They'd been preparing the Daedalus for its return journey all day, personnel coming and going, but now he watched as one by one the flag draped coffins of the dead were carried solemnly out, the pier lined with people paying their respects. No one had told him. He should have been down there but they'd not even told him. He thumped his good hand down on the railing and watched as the photograph slipped from his grip and was swept out across the ocean by the wind.

ooOoo

"John, you cannot be serious." Elizabeth looked at him in disbelief and then to Carson, looking for back-up.

"Aye son, you're still not well," provided the doctor. "You need your rest."

"I know that. I'm not asking you to let me go base jumping; I'll be taking it easy and I'll do everything I'm told but I need to do this."

"John, I know we should have told you about the ceremony but you attended the memorial service and you have had a stressful couple of days." He could see the worry lines on her face but he had to convince her, he had to do this.

"I'm not going to pretend I'm not pissed about that, you should have told me and I should have been there but this is not some kind of knee jerk reaction. I've thought long and hard about this and it's the one thing I can do for them. Elizabeth, please." He pleaded, knowing that at the end of the day it would be her choice. "I was their commanding officer, let me take them home. Let me go back to Earth."


	20. Bad Penny

_A/N:- Well here we are the final chapter, there is a short epilogue to come after this and I'll get that posted as soon as possible._

_Thank you so much for sticking with me this was my first ever fic and a lot of mistakes have been made along the way but I've also learnt a great deal. Thank you to everyone who has been kind enough to leave reviews and most of all thank you to Alipeeps for her invaluable betaing skills._

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* * *

****Chapter 19**

**Bad Penny**

The shiny brass plaque read Lieutenant Edward James Ripley 1978-2006. Snow fell lightly as they lowered the coffin into the ground; it was the fifth funeral he had attended in three days, three of them here at Arlington. At each interment he had stood silently at the grave, watching the desolate grief of the families as they tried to come to terms with the loss of their sons and daughters, never knowing how, or where, they had died.

He had visited McCormack and Benedict's families, unable to tell them anything about what their loved ones had been doing, unable to give McCormack's family the comfort of being able to bury their son. Over the last week he had found himself repeating an endless list of platitudes; he found the words 'bravery' and 'courage' spilling from his lips over and over again until they had become empty of meaning. Ed Ripley had been a good man, smart, well-liked and had an endless supply of dirty jokes. Promotion had been beckoning for him. John had told his parents that; Ed's father had shook his hand and thanked him, his mother had barely concealed her hatred. The Air Force had taken her child and she wanted nothing more to do with them.

Walking back across the cemetery, his feet crunching on the gravel and his eyes cast downward, watching the snow melting against his uniform, he caught sight of his reflection in the tinted windows of one of the funeral cars. A tired and drawn face stared back at him and the dress uniform only served to accentuate his weight loss. He felt a heavy hand on his shoulder and in the car window he could see the reflection of General Landry standing behind him.

"You look tired John, you should go back to your hotel and get some rest. Mrs Ripley has asked that only friends and family attend the wake."

"Can't say I blame them."

"I guess I'll see you tomorrow. Are you sure you up to all this, John? Believe me, you don't want to suffer the wrath of my daughter if you over do things."

"I'll be okay. It's something I need to do, Sir." The General nodded solemnly and patted him on the back.

"Get some rest."

"Thank you, Sir."

He watched everyone else leave before climbing into the car beside the young Corporal who had been assigned as his driver.

"Back to the hotel, Sir?" she asked.

"No. Um…" He held out the scrap of paper with the address on. "You know where this is?" She studied the address for a moment.

"Yes Sir." The young woman turned the key in the ignition and pulled away. Sensing his mood, she kept quiet, letting him watch the streets passing through the window. It was eerie being back on Earth, there was an almost dream-like feel to it. Atlantis was the real world for him now. What did it say about him that he could only find a home in another galaxy? Resting his head against the window, he watched as the snow fell faster and the clouds turned a bluish-grey, throwing the world into twilight. Christmas lights twinkled on shop fronts and were wound around the branches of leafless trees. It hadn't even occurred to him that it was almost Christmas until he had seen a forlorn looking artificial tree that someone had stuck on a desk in one of the SGC labs. Now, seeing signs of the holiday season all around him, he found himself feeling lonelier than ever.

ooOoo

Tiredness overwhelmed him and he struggled to keep his eyes open but at some point he must have lost the fight and he found himself being woken up by the Corporal's gentle touch on his shoulder. She smiled apologetically as he rubbed the sleep out of his eyes with the heel of his hand.

"Would you like me to wait, Sir?" John looked out of the window at the picture book suburban home, resolve fighting with the butterflies in his stomach.

"No." It was too late to change his mind now. "You can go, I'll get a taxi back. Thank you, Corporal."

"You're welcome, Sir." He got out of the car and, placing his cap back on his head, stood facing a house he'd never seen before; his father had moved yet again while he was in Antarctica. His childhood had consisted of one move after another as his father went where the air force sent him, they'd lived in a dozen different states and had spent time in England and Germany; his adult life had followed a similar path, never staying in one place for too long. Atlantis was the closest thing he'd ever had to a permanent home. Apparently his stepmother had finally convinced his father to settle down; Tom Sheppard had spent time at The Pentagon during the height of the Cold War and obviously something about the area had drawn him back.

Taking a deep and calming breath, he headed toward the front door. As he rang the bell he cursed Elizabeth under his breath for putting such a stupid idea as this into his head. A moment later the door opened and he found himself face to face with his father for the first time in five years. The older man stood with his mouth open for a few moments, a thousand different emotions playing over his face, before he finally spoke.

"You look like crap!" All the times John had imagined this moment, playing through a thousand different scenes in his head, he'd never come up with a scenario where those would be his father's opening words.

John struggled to come up with a response and eventually settled for a sarcastic, "Thanks."

They stood looking at each other, neither sure what to say; eventually the fact that John was freezing his ass off was the deciding factor. "Can I come in, please?" Tom Sheppard shook himself out of his surprise and held the door was open wider for John and he followed his father down the hall to the lounge. They both stood there awkwardly; as though they were strangers. The change in temperature was dramatic, the cold outside replaced with a wave of heat coming from an open fire. Taking off his cap, John bent to lay it on the coffee table and couldn't help but notice the fleeting expression on his fathers face when he saw the thin scar running through his still short hair. He'd seen the same expression on other people's faces and would be grateful when his hair had grown back enough to cover it.

"Didn't think I'd be seeing you again," his father said. "Thought you really had gone and got yourself killed this time."

"You weren't the only one."

"Are you gonna to sit down? You look exhausted."

"Yeah, I am. It's been a long week." He was finding his slow recovery maddening; he'd always been an athletic person and to find himself exhausted from walking up a flight of stairs or simply standing up for any length of time was both embarrassing and frustrating. Un-buttoning his jacket and loosening his tie, he sat down on the sofa, sighing in relief.

"I know it's a little early in the evening but do you want a drink? God knows, I need one." John's father reached a bottle of Scotch down from the dresser.

"I'm still on some pretty heavy duty painkillers, got to stick to the soft stuff."

"There's coffee in the pot." John felt a bitter amusement at the forced politeness, as though they were strangers.

"I'm good, thanks."

"Do you mind if I do?"

"No, go for it." Tom Sheppard poured, paused for a moment, and poured the same in again. Looking at his son, he shrugged. "Like I said, I need a drink. When that bell rang you were the last person I expected to see on the other side of the door."

"I nearly didn't come."

"Why did you?"

"Honestly? A bunch of reasons. I was in the neighbourhood anyway." He tugged at the lapel of the jacket of his dress uniform. "Arlington." It was the only explanation he needed to give. "Elizabeth showed me the photograph you sent her. I thought maybe it meant…I thought maybe it meant… you'd want to see me."

His father took a seat in the chair opposite John. "I did…I do. I'm glad you came. So…do you think we can have a conversation without arguing?"

"I'd like to think so." He meant that. It would be nice if they could just talk. John looked around the room; familiar furniture in a strange house. "So, how is everything?"

For the next few minutes they sat and talked like strangers, exchanging pleasantries, doing everything but talking about the weather, and John felt his heart sink. There really was nothing left for him here.

"So, what happened?" the older man asked eventually. "You were captured?" He said it as if he were asking someone about their day at the office.

"Yeah."

"But you can't tell me who was holding you?" John forced an apologetic smile.

"No. You know how it is."

"Yes, I know how it is." Even so John could see the old man's frustration at not knowing. He looked John up and down. "I'm guessing whoever these people were, they hadn't heard of the Geneva Convention."

"No." You don't know how true that is, thought John.

"Was it bad, John?" He was taken aback by the softness in his father's voice.

"Yeah," he nodded. There was no point in denying it. "It was bad."

"Are you going to be okay?"

"I'm healing slowly, getting the weight back on." Tom Sheppard cleared his throat and shifted in his chair.

"That's not what I meant. Are you…" John could see his father fighting for the words, uncomfortable with the question.

"Mentally unstable?" John laughed bitterly. "Well that's the million dollar question, isn't it?" He paused, swallowing back. "There's always been a bit of a question mark over my command and this…it's just given them more reason to doubt me. There's a Colonel who knows the situation nearly as well as I do, he's a good man. I'm not supposed to know but they're considering putting him in above me. A lot of people would have had it that way from the start."

"But they gave the job to you."

"Only by default, my commanding officer was…killed." He sighed, leaning back into the sofa. "I was just the highest ranking officer in the field. And Elizabeth fought my corner, so they promoted me. No one ever intended for me to be in command. I wasn't even meant to be part of the operation, it all just kind of happened."

"Yet you've been doing this for two and a half years and, according to Doctor Weir, you're damn good at it."

"I'm just not sure I'm the right man for the job anymore; not sure I ever was." His father sighed heavily.

"And here was me thinking you'd finally stopped running away from your responsibilities." John leaned his head back and looked at the ceiling.

"I'm not running away!" He raised his voice without meaning to. He should have known they couldn't last a whole conversation without an argument. "I don't have any control over this."

"Like hell you don't. You prove to them you're the right man."

"What if I'm not?" The words came out harsher than John intended and he lowered his eyes, meeting his fathers gaze.. "I never asked for any of this, I just got lucky. I'm still the same screw up you always said I was." He felt his voice faltering. "I'm not the man they think I am."

"Since when did you give a crap what anyone else thought?"

"It matters what these people think. They rely on me, trust me, care about me. When I make a mistake, bad things happen to a lot of people."

"Then don't make mistakes."

"It's not that simple. I…I don't know if I can do it anymore." He scrubbed his hand through his short hair. "They changed me…took something away and I don't know how to get it back."

"You can't. You've just got to learn to let it go."

"Well, gee, thanks Dad. That makes me feel so much better." John couldn't keep the venom from his voice.

"What do you want from me, John?" Tom Sheppard leaned forward in his chair.

"Tell me what to do, tell me how I fix this." John thumped his good hand against his chest, still feeling the healing ribs.

"I can't."

"Dad, I'm broken." His voice was almost pleading.

"And the only one who can fix you is you." John lent forward and put his head in his hands, wondering what the hell he was doing here and fighting back the emotions that threatened to overwhelm him. "Tell me this, if you go back to wherever the hell you've been and three of your men are trapped behind enemy lines and this Colonel tells you to return to base without them, what are you going to do, John? I'll tell you what you'll do; exactly what you did in Afghanistan, consequences be damned." The older Colonel Sheppard sat back in his chair. "Can you really go back and take orders from this guy without question?"

"No." He didn't need to think about the answer, it was just there; he knew that if it came down to a choice between doing what he thought was right and disobeying a direct order, he'd make the same choices again.

"Then you've got two options. You go back and you do your job, or you walk away. Which one is it going to be, Colonel?"

OoOoo

John stood at the door watching the snow fall in front of the headlights of the taxi. Big heavy flakes still drifted down and the ground was now covered with a thick layer. His stepmother had come home to find them both sitting silently in the lounge. There'd been a few tears on her part and she had busied around them with forced jollity, sensing the uncomfortable atmosphere. In truth, John just felt drained and detached. He had answered her questions and smiled patiently when she emptied the contents of the refrigerator in an attempt to force feed him as much food as possible.

Now he stood outside the front door, adjusting his cap back onto his head; the snow had proven a good excuse to not stay late. He turned back to his father, still standing at the door.

"I had a pretty high security clearance back in the day, you know that?" he said.

"Yes, Sir." John answered. Tom Sheppard had been involved in classified operations during the Cold War, a fact he was immeasurably proud of.

"I still have a lot of friends in high places, The Pentagon for example." John resisted the temptation to zone out, he'd heard this all before. "I tried to call in a few old favours, find out what exactly you've been doing these last few years. I figured that it was some UN 'lets all be friends' kind of gig." He waved his hand dismissively.

"What did you find out?" John asked, genuinely curious. His father frowned and fixed him with a stare, the first time he'd looked him full in the face since he'd first opened the door.

"Nothing," he admitted reluctantly. "Whatever the hell you've got yourself into, it's big isn't it?" John couldn't help but smile. It felt good to have one over on the old man for a change, it was petty of him he knew, but for a moment he was going to enjoy the feeling.

"Doesn't come any bigger." His father studied him intensely for a moment.

"You know, over the years I've heard some pretty crazy conspiracy theories."

"Yeah, me too but you know what they say, truth is stranger than fiction." They stood looking at one another for a moment longer, the taxi's engine the only sound.

"I'm not going to see you again, am I?" his father asked.

"No. Probably not." Tom Sheppard nodded sadly in understanding. The old man swallowed back and smiled.

"You know, I'm proud of you, Lieutenant Colonel Sheppard."

"Yeah," John said bitterly. "But I never wanted you to be proud of my rank, I wanted you to be proud of your son. Goodbye, Dad." He walked away without looking back.


	21. Epilogue

**Epilogue**

_Don't walk in front of me, I may not follow. Don't walk behind me, I may not lead. Just walk beside me and be my friend. - Albert Camus_

It was early and the pale light glinted off the water below and the breeze coming through the open window was crisp and cool; he could taste the tang of salt on his lips. Stepping back from the window, he looked down at the holstered gun lying on the bed. Picking it up, he felt the weight in his hand. He looped the holster onto his belt and fastened the straps around his thigh. The light pressure against his leg was strangely comforting.

Leaving his quarters, he headed through the corridors, passing a scientist who mumbled a 'hello', never raising his head from the data pad in his hand. Stepping into the transporter, he punched his destination and stepped out into another bright and airy corridor. The door to the armoury opened for him and the Sergeant on duty greeted him cheerfully. He was expected and the P-90 and ammo was laid out for him next to his vest. He signed the weapon out before heading back to the transporter.

As he stepped out of the transporter, he saw Elizabeth standing on the balcony overlooking the gate room; she was waiting for him, he knew. She turned with a beaming smile, just a little too strained to be totally genuine. She was worried about him but trying not to show it.

"Good morning, Colonel," she said brightly.

"Dr Weir." He joined her at the railing. Down in the gate room, his team were preparing to leave, Ronon's stillness only serving to exaggerate McKay's nervous energy as he checked his equipment, talking to himself the whole time. Teyla glanced up at them and smiled.

"Shall I start dialing the gate, Sir?" the technician asked. John looked toward him and nodded, not quite trusting his voice to carry across the room without betraying his nerves. He watched as the chevrons locked themselves into place and the wormhole exploded outward before settling back into the familiar shimmering pool. Elizabeth placed her hand over his on the railing and squeezed it gently.

"Are you sure you're ready for this?"

"Kate seems to think I am."

"And what do you think?"

"I think she's right. Still mildly terrified though. I know this is routine mission but I learnt the hard way there's no such thing as safe out here."

"It's not too late to back out, if you want to wait a few more days..." But he knew it was too late, if he didn't do this now, he was scared he'd never be able to.

"No. No, I'm good."

"Um…excuse me," McKay called up to him, "but we're waiting here and if I have to go on this utterly pointless trade run, I'd really like to get going sometime this morning. There's rumours of real cheesecake for dinner and last time that happened Ronon got into a fight with that market trader on MR5 834 and by the time we got back there was only lemon left. I swear he does it on purpose."

"I didn't get into a fight," Ronon argued.

"You knocked the guy out cold."

"He started it."

"Oh, now there's an intelligent argument." McKay rolled his eyes.

"He insulted Teyla."

"And it was very kind of you to intervene Ronon but I am quite capable of looking after myself," Teyla said forcefully.

John watched from the balcony as the three of them continued to bicker and felt a smile spread across his face. Letting go of the railings, he turned to Elizabeth.

"Yeah, I'm good." And as he walked down the stairs toward the gate, he realised he meant it.

Fin


End file.
